Query 040555
Match_columns 313
No_of_seqs 274 out of 1141
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 09:33:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040555.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040555hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07526 POX: Associated with 99.9 6.6E-27 1.4E-31 201.5 6.7 61 14-74 79-139 (140)
2 KOG0775 Transcription factor S 99.9 9.4E-26 2E-30 210.5 14.4 115 53-174 114-232 (304)
3 KOG0773 Transcription factor M 99.9 2.5E-26 5.5E-31 220.9 8.7 173 16-188 124-312 (342)
4 smart00574 POX domain associat 99.9 3.2E-25 6.9E-30 189.7 7.3 64 11-74 74-139 (140)
5 PF05920 Homeobox_KN: Homeobox 99.7 1.1E-16 2.3E-21 110.7 4.6 40 133-172 1-40 (40)
6 KOG0774 Transcription factor P 99.6 6.2E-15 1.3E-19 137.7 11.8 65 115-179 188-252 (334)
7 cd00086 homeodomain Homeodomai 99.5 1.3E-13 2.9E-18 99.4 7.2 57 117-176 2-58 (59)
8 PF00046 Homeobox: Homeobox do 99.5 1.2E-13 2.6E-18 100.1 6.5 57 116-175 1-57 (57)
9 smart00389 HOX Homeodomain. DN 99.4 3.1E-13 6.7E-18 97.0 7.0 54 118-174 3-56 (56)
10 KOG0487 Transcription factor A 99.0 2.1E-10 4.6E-15 110.3 4.0 63 115-180 234-297 (308)
11 KOG0842 Transcription factor t 99.0 3.6E-10 7.8E-15 108.6 3.8 65 115-182 152-217 (307)
12 KOG0843 Transcription factor E 98.9 1.7E-09 3.8E-14 96.8 7.1 63 115-180 102-164 (197)
13 KOG0489 Transcription factor z 98.9 6.3E-10 1.4E-14 104.8 4.3 60 115-177 159-218 (261)
14 KOG0850 Transcription factor D 98.9 4.6E-09 9.9E-14 97.1 8.5 64 112-178 119-182 (245)
15 KOG0488 Transcription factor B 98.9 7.1E-09 1.5E-13 100.1 9.9 59 118-179 175-233 (309)
16 KOG0493 Transcription factor E 98.9 4.1E-09 9E-14 99.1 6.6 61 113-176 244-304 (342)
17 KOG0483 Transcription factor H 98.8 2.9E-09 6.4E-14 96.9 5.3 67 115-184 50-116 (198)
18 TIGR01565 homeo_ZF_HD homeobox 98.8 9.8E-09 2.1E-13 76.6 5.3 52 116-170 2-57 (58)
19 KOG0484 Transcription factor P 98.8 2.2E-08 4.8E-13 82.8 7.1 60 118-180 20-79 (125)
20 KOG0485 Transcription factor N 98.8 7.3E-09 1.6E-13 95.3 4.5 64 114-180 103-166 (268)
21 COG5576 Homeodomain-containing 98.7 1.3E-08 2.8E-13 89.6 5.2 61 114-177 50-110 (156)
22 KOG0848 Transcription factor C 98.6 1.9E-08 4.1E-13 94.9 3.9 56 122-180 206-261 (317)
23 KOG2251 Homeobox transcription 98.6 3.2E-08 6.9E-13 91.1 4.8 61 114-177 36-96 (228)
24 KOG0492 Transcription factor M 98.6 4.3E-08 9.3E-13 89.7 5.5 62 114-178 143-204 (246)
25 KOG3802 Transcription factor O 98.6 3.3E-08 7.2E-13 97.5 3.1 58 116-176 295-352 (398)
26 KOG0491 Transcription factor B 98.4 9.8E-08 2.1E-12 84.7 2.5 57 119-178 104-160 (194)
27 KOG0494 Transcription factor C 98.4 2.9E-07 6.2E-12 86.8 5.0 55 120-177 146-200 (332)
28 KOG0486 Transcription factor P 98.4 2.5E-07 5.4E-12 89.1 4.0 59 120-181 117-175 (351)
29 KOG4577 Transcription factor L 98.3 5.4E-07 1.2E-11 86.0 3.7 61 112-175 164-224 (383)
30 KOG2252 CCAAT displacement pro 98.3 1.6E-06 3.5E-11 88.6 7.1 56 115-173 420-475 (558)
31 KOG0847 Transcription factor, 98.1 2.3E-06 5E-11 79.2 4.6 62 120-184 172-233 (288)
32 KOG0844 Transcription factor E 98.0 2.1E-06 4.5E-11 82.7 1.4 62 115-179 181-242 (408)
33 KOG0849 Transcription factor P 97.8 3.1E-05 6.7E-10 76.3 5.7 63 113-178 174-236 (354)
34 KOG0490 Transcription factor, 97.7 1.8E-05 4E-10 71.2 2.1 61 114-177 59-119 (235)
35 KOG1168 Transcription factor A 97.3 7.1E-05 1.5E-09 71.9 0.7 59 114-175 308-366 (385)
36 KOG0773 Transcription factor M 97.2 0.00019 4.1E-09 69.6 2.3 59 118-177 98-156 (342)
37 PF11569 Homez: Homeodomain le 96.9 0.00089 1.9E-08 49.8 3.2 43 127-172 10-52 (56)
38 KOG0490 Transcription factor, 96.6 0.0029 6.4E-08 56.9 4.9 62 113-177 151-212 (235)
39 KOG1146 Homeobox protein [Gene 93.4 0.06 1.3E-06 60.7 3.2 56 120-178 908-963 (1406)
40 KOG3623 Homeobox transcription 86.1 1.3 2.8E-05 48.0 5.5 44 127-173 568-611 (1007)
41 PF04218 CENP-B_N: CENP-B N-te 84.6 2.1 4.6E-05 31.0 4.5 46 117-170 2-47 (53)
42 cd06171 Sigma70_r4 Sigma70, re 75.8 8.3 0.00018 25.5 4.9 45 122-174 11-55 (55)
43 PF04545 Sigma70_r4: Sigma-70, 74.0 6.8 0.00015 27.2 4.2 47 121-175 4-50 (50)
44 PF08281 Sigma70_r4_2: Sigma-7 73.0 7.3 0.00016 27.3 4.2 45 121-173 10-54 (54)
45 PF13443 HTH_26: Cro/C1-type H 68.1 15 0.00033 26.3 5.1 37 130-173 2-38 (63)
46 PRK09642 RNA polymerase sigma 67.7 9.4 0.0002 32.1 4.5 51 121-179 106-156 (160)
47 PF01527 HTH_Tnp_1: Transposas 66.4 9.9 0.00022 28.2 3.9 46 117-170 2-48 (76)
48 KOG0809 SNARE protein TLG2/Syn 66.1 13 0.00029 36.4 5.6 77 5-81 90-171 (305)
49 cd00569 HTH_Hin_like Helix-tur 63.7 23 0.0005 20.6 4.7 38 121-166 5-42 (42)
50 PRK06759 RNA polymerase factor 60.4 19 0.00041 29.9 5.0 47 121-175 106-152 (154)
51 PRK12530 RNA polymerase sigma 59.8 23 0.00049 31.1 5.6 53 121-181 134-186 (189)
52 TIGR02985 Sig70_bacteroi1 RNA 58.6 22 0.00047 29.3 5.0 48 121-176 113-160 (161)
53 PRK12512 RNA polymerase sigma 58.4 18 0.00039 31.2 4.7 49 121-177 131-179 (184)
54 PRK09644 RNA polymerase sigma 57.7 24 0.00053 29.9 5.3 50 120-177 107-156 (165)
55 TIGR02939 RpoE_Sigma70 RNA pol 57.1 17 0.00037 31.2 4.3 49 121-177 138-186 (190)
56 TIGR02937 sigma70-ECF RNA poly 56.2 23 0.00051 28.1 4.7 48 121-176 110-157 (158)
57 PRK11924 RNA polymerase sigma 56.1 28 0.0006 29.2 5.4 49 122-178 126-174 (179)
58 PRK09646 RNA polymerase sigma 55.6 24 0.00052 31.0 5.1 49 121-177 142-190 (194)
59 PRK00118 putative DNA-binding 55.0 29 0.00062 28.8 5.1 48 121-176 17-64 (104)
60 PRK12526 RNA polymerase sigma 54.7 25 0.00055 31.3 5.1 49 121-177 153-201 (206)
61 PRK09652 RNA polymerase sigma 54.3 31 0.00067 29.0 5.4 49 121-177 128-176 (182)
62 TIGR02948 SigW_bacill RNA poly 53.8 20 0.00044 30.7 4.3 49 121-177 136-184 (187)
63 PRK12514 RNA polymerase sigma 53.2 29 0.00063 29.8 5.1 48 121-176 129-176 (179)
64 PRK12520 RNA polymerase sigma 52.7 35 0.00076 29.7 5.6 52 121-180 131-182 (191)
65 PRK12531 RNA polymerase sigma 52.7 23 0.00049 31.1 4.4 51 121-179 141-191 (194)
66 PRK06930 positive control sigm 52.5 31 0.00068 30.6 5.3 55 121-183 114-168 (170)
67 PRK12547 RNA polymerase sigma 51.9 24 0.00052 30.0 4.3 49 121-177 112-160 (164)
68 PRK09648 RNA polymerase sigma 51.3 33 0.00071 29.8 5.2 49 121-177 139-187 (189)
69 PF13518 HTH_28: Helix-turn-he 51.3 18 0.00039 24.7 2.9 25 147-171 14-38 (52)
70 PRK08583 RNA polymerase sigma 50.8 28 0.00061 32.1 4.9 49 121-177 205-253 (257)
71 smart00421 HTH_LUXR helix_turn 50.7 61 0.0013 21.6 5.5 47 121-176 3-49 (58)
72 PRK12519 RNA polymerase sigma 50.6 31 0.00067 30.0 4.9 49 121-177 141-189 (194)
73 PRK12515 RNA polymerase sigma 50.5 40 0.00086 29.3 5.6 49 121-177 131-179 (189)
74 TIGR03001 Sig-70_gmx1 RNA poly 49.7 31 0.00068 32.1 5.1 53 121-181 161-213 (244)
75 PRK06811 RNA polymerase factor 49.5 30 0.00065 30.2 4.7 49 121-177 131-179 (189)
76 TIGR02983 SigE-fam_strep RNA p 49.2 27 0.00059 29.3 4.2 49 121-177 110-158 (162)
77 PRK12541 RNA polymerase sigma 48.9 25 0.00055 29.6 4.0 47 121-175 112-158 (161)
78 PRK03975 tfx putative transcri 48.8 24 0.00052 30.8 3.9 51 120-179 5-55 (141)
79 PRK05602 RNA polymerase sigma 48.7 34 0.00074 29.6 4.9 48 122-177 129-176 (186)
80 TIGR02999 Sig-70_X6 RNA polyme 48.7 39 0.00083 29.0 5.2 47 122-176 135-181 (183)
81 TIGR02989 Sig-70_gvs1 RNA poly 48.4 37 0.0008 28.2 4.9 47 121-175 111-157 (159)
82 PRK12544 RNA polymerase sigma 48.1 45 0.00098 29.9 5.7 53 121-181 148-200 (206)
83 PRK12536 RNA polymerase sigma 47.7 31 0.00067 29.9 4.4 48 122-177 130-177 (181)
84 TIGR02941 Sigma_B RNA polymera 47.3 31 0.00066 31.8 4.6 49 121-177 205-253 (255)
85 PF04967 HTH_10: HTH DNA bindi 47.0 55 0.0012 23.9 4.9 46 122-168 1-46 (53)
86 PRK09047 RNA polymerase factor 46.6 49 0.0011 27.5 5.4 50 120-177 105-154 (161)
87 PRK09639 RNA polymerase sigma 46.5 46 0.00099 27.9 5.2 48 121-177 112-159 (166)
88 PRK12532 RNA polymerase sigma 46.2 34 0.00074 29.9 4.5 50 121-178 136-185 (195)
89 PRK06986 fliA flagellar biosyn 45.8 26 0.00057 31.9 3.8 49 121-177 184-232 (236)
90 PRK12523 RNA polymerase sigma 45.7 35 0.00075 29.2 4.4 49 121-177 119-167 (172)
91 TIGR02954 Sig70_famx3 RNA poly 45.7 43 0.00094 28.4 5.0 49 121-177 119-167 (169)
92 PRK12516 RNA polymerase sigma 44.9 38 0.00083 29.8 4.6 50 121-178 116-165 (187)
93 PRK04217 hypothetical protein; 44.6 54 0.0012 27.5 5.2 49 121-177 42-90 (110)
94 TIGR02980 SigBFG RNA polymeras 44.1 41 0.00089 30.2 4.8 49 121-177 178-226 (227)
95 PF00196 GerE: Bacterial regul 43.6 50 0.0011 23.5 4.3 51 121-180 3-53 (58)
96 PRK12546 RNA polymerase sigma 43.1 34 0.00074 30.2 4.0 49 121-177 113-161 (188)
97 PRK13919 putative RNA polymera 42.9 44 0.00096 28.7 4.7 49 121-177 135-183 (186)
98 PRK09647 RNA polymerase sigma 42.9 49 0.0011 29.6 5.1 49 121-177 138-186 (203)
99 PRK12513 RNA polymerase sigma 42.6 24 0.00051 30.8 2.9 49 121-177 139-187 (194)
100 PRK12524 RNA polymerase sigma 42.0 54 0.0012 28.8 5.1 49 121-177 136-184 (196)
101 TIGR02943 Sig70_famx1 RNA poly 41.7 70 0.0015 28.0 5.8 51 121-179 131-181 (188)
102 PF12998 ING: Inhibitor of gro 41.7 1.3E+02 0.0028 23.6 6.9 69 8-78 13-82 (105)
103 TIGR02479 FliA_WhiG RNA polyme 41.4 46 0.001 30.0 4.7 48 121-176 175-222 (224)
104 PRK12543 RNA polymerase sigma 41.4 70 0.0015 27.5 5.7 52 121-180 117-168 (179)
105 PRK12542 RNA polymerase sigma 41.4 40 0.00087 29.2 4.2 49 121-177 122-170 (185)
106 PF10668 Phage_terminase: Phag 41.3 24 0.00052 26.7 2.3 20 147-166 24-43 (60)
107 PRK12533 RNA polymerase sigma 40.8 47 0.001 30.3 4.7 49 121-177 134-182 (216)
108 PRK12537 RNA polymerase sigma 40.6 58 0.0012 28.2 5.0 48 121-176 133-180 (182)
109 PRK15369 two component system 40.5 92 0.002 25.7 6.1 49 121-178 149-197 (211)
110 cd01392 HTH_LacI Helix-turn-he 40.1 29 0.00063 23.8 2.5 21 150-170 2-22 (52)
111 PRK12545 RNA polymerase sigma 39.9 67 0.0015 28.4 5.4 50 121-178 139-188 (201)
112 PRK11511 DNA-binding transcrip 39.7 72 0.0016 26.5 5.3 43 123-169 7-49 (127)
113 PRK12522 RNA polymerase sigma 39.4 65 0.0014 27.5 5.1 51 121-179 119-169 (173)
114 PRK09645 RNA polymerase sigma 39.3 46 0.00099 28.3 4.1 49 121-177 118-166 (173)
115 PF13384 HTH_23: Homeodomain-l 38.9 30 0.00064 23.7 2.4 24 147-170 19-42 (50)
116 PRK12538 RNA polymerase sigma 38.3 71 0.0015 29.4 5.5 50 121-178 171-220 (233)
117 PRK09649 RNA polymerase sigma 37.7 47 0.001 29.0 4.1 47 121-175 130-176 (185)
118 PRK12539 RNA polymerase sigma 37.6 70 0.0015 27.7 5.1 49 121-177 131-179 (184)
119 PRK09641 RNA polymerase sigma 36.9 71 0.0015 27.3 5.0 49 121-177 136-184 (187)
120 PF01381 HTH_3: Helix-turn-hel 36.7 30 0.00064 24.0 2.1 22 147-168 11-32 (55)
121 PRK08295 RNA polymerase factor 36.2 62 0.0013 28.3 4.6 47 121-176 155-201 (208)
122 PRK12535 RNA polymerase sigma 36.1 63 0.0014 28.7 4.7 49 121-177 133-181 (196)
123 PRK07037 extracytoplasmic-func 35.9 84 0.0018 26.3 5.2 49 121-177 109-157 (163)
124 PRK12527 RNA polymerase sigma 35.7 84 0.0018 26.3 5.2 49 121-177 105-153 (159)
125 PRK09413 IS2 repressor TnpA; R 35.5 1.1E+02 0.0023 25.4 5.6 46 118-170 9-54 (121)
126 PRK11923 algU RNA polymerase s 35.5 74 0.0016 27.6 4.9 48 122-177 139-186 (193)
127 PF14943 MRP-S26: Mitochondria 35.5 42 0.0009 30.2 3.4 24 22-45 27-50 (170)
128 TIGR02959 SigZ RNA polymerase 35.1 98 0.0021 26.5 5.6 49 121-177 100-148 (170)
129 TIGR02393 RpoD_Cterm RNA polym 35.1 90 0.0019 28.5 5.6 56 121-180 176-231 (238)
130 PRK08301 sporulation sigma fac 35.0 85 0.0018 28.4 5.4 53 121-177 178-230 (234)
131 PF07638 Sigma70_ECF: ECF sigm 35.0 78 0.0017 27.9 5.0 48 122-177 136-183 (185)
132 PRK12517 RNA polymerase sigma 35.0 1.2E+02 0.0026 26.6 6.2 52 121-180 128-179 (188)
133 TIGR02859 spore_sigH RNA polym 34.7 66 0.0014 27.8 4.5 30 147-176 167-196 (198)
134 PRK09637 RNA polymerase sigma 34.7 89 0.0019 27.2 5.3 49 121-177 106-154 (181)
135 PRK12529 RNA polymerase sigma 34.6 78 0.0017 27.4 4.9 47 121-175 127-173 (178)
136 PRK07670 RNA polymerase sigma 34.3 86 0.0019 28.9 5.4 48 121-176 201-248 (251)
137 PRK12540 RNA polymerase sigma 34.0 63 0.0014 28.3 4.3 50 121-178 111-160 (182)
138 PRK07408 RNA polymerase sigma 33.9 71 0.0015 29.7 4.8 50 121-178 203-252 (256)
139 PRK09415 RNA polymerase factor 33.8 69 0.0015 27.7 4.4 49 121-177 127-175 (179)
140 TIGR03070 couple_hipB transcri 33.7 33 0.00071 23.5 1.9 23 148-170 18-40 (58)
141 PRK12518 RNA polymerase sigma 33.4 45 0.00097 28.4 3.1 48 122-177 121-168 (175)
142 cd07597 BAR_SNX8 The Bin/Amphi 33.3 1.9E+02 0.0041 27.1 7.5 70 10-79 34-113 (246)
143 COG3413 Predicted DNA binding 33.1 84 0.0018 28.5 5.0 52 121-173 155-206 (215)
144 PRK12511 RNA polymerase sigma 32.8 74 0.0016 27.9 4.5 49 121-177 111-159 (182)
145 PRK06288 RNA polymerase sigma 32.3 99 0.0021 28.8 5.5 49 121-177 212-260 (268)
146 PRK12528 RNA polymerase sigma 32.3 97 0.0021 26.0 5.0 46 121-174 113-158 (161)
147 cd06170 LuxR_C_like C-terminal 32.3 92 0.002 20.9 4.1 45 122-175 1-45 (57)
148 PRK12534 RNA polymerase sigma 31.1 1E+02 0.0022 26.6 5.0 48 121-176 137-184 (187)
149 cd00093 HTH_XRE Helix-turn-hel 30.6 46 0.001 21.3 2.2 23 148-170 15-37 (58)
150 PRK07122 RNA polymerase sigma 30.4 77 0.0017 29.8 4.4 48 121-176 215-262 (264)
151 cd00131 PAX Paired Box domain 29.9 1.9E+02 0.0041 24.4 6.3 46 121-169 75-127 (128)
152 TIGR02392 rpoH_proteo alternat 29.7 76 0.0017 29.7 4.3 50 121-176 218-267 (270)
153 TIGR02952 Sig70_famx2 RNA poly 29.5 1.1E+02 0.0024 25.5 4.9 47 121-175 122-168 (170)
154 TIGR02885 spore_sigF RNA polym 29.3 1E+02 0.0022 27.8 4.9 48 121-176 183-230 (231)
155 COG0133 TrpB Tryptophan syntha 28.6 4.5E+02 0.0098 26.7 9.4 52 15-67 19-70 (396)
156 PRK10072 putative transcriptio 28.2 42 0.00091 27.4 2.0 24 147-170 48-71 (96)
157 PRK05657 RNA polymerase sigma 27.8 1.2E+02 0.0027 29.4 5.5 53 121-177 262-314 (325)
158 TIGR02947 SigH_actino RNA poly 27.7 76 0.0016 27.6 3.7 50 121-178 131-180 (193)
159 PRK09651 RNA polymerase sigma 27.2 1.1E+02 0.0023 26.2 4.5 48 121-176 119-166 (172)
160 PRK09640 RNA polymerase sigma 27.2 46 0.00099 29.0 2.2 48 122-177 135-182 (188)
161 smart00530 HTH_XRE Helix-turn- 26.8 57 0.0012 20.7 2.1 23 148-170 13-35 (56)
162 PRK12525 RNA polymerase sigma 26.5 1.2E+02 0.0025 25.9 4.5 47 121-175 118-164 (168)
163 TIGR02960 SigX5 RNA polymerase 26.4 94 0.002 29.3 4.3 49 121-177 142-190 (324)
164 TIGR02950 SigM_subfam RNA poly 25.9 73 0.0016 26.3 3.1 46 122-175 106-151 (154)
165 TIGR02846 spore_sigmaK RNA pol 25.6 1.2E+02 0.0026 27.4 4.7 52 121-176 174-225 (227)
166 PF01726 LexA_DNA_bind: LexA D 25.0 1.4E+02 0.003 22.5 4.1 41 121-166 3-47 (65)
167 PF13411 MerR_1: MerR HTH fami 24.6 61 0.0013 23.4 2.1 19 149-167 4-22 (69)
168 PRK08215 sporulation sigma fac 24.6 1.4E+02 0.003 27.6 5.0 49 121-177 209-257 (258)
169 cd04761 HTH_MerR-SF Helix-Turn 24.4 74 0.0016 21.3 2.4 19 149-167 4-22 (49)
170 PHA01976 helix-turn-helix prot 24.4 60 0.0013 23.4 2.1 23 148-170 18-40 (67)
171 smart00319 TarH Homologues of 24.3 2.6E+02 0.0057 22.2 6.1 67 7-77 51-127 (135)
172 PRK05803 sporulation sigma fac 23.7 1.5E+02 0.0032 27.0 4.9 54 121-178 175-228 (233)
173 TIGR02835 spore_sigmaE RNA pol 23.6 1.2E+02 0.0027 27.5 4.4 53 121-177 178-230 (234)
174 PF12844 HTH_19: Helix-turn-he 23.4 1.1E+02 0.0024 21.7 3.3 30 147-177 14-43 (64)
175 PF04740 LXG: LXG domain of WX 23.3 4.5E+02 0.0098 23.1 7.9 56 15-72 6-61 (204)
176 TIGR02607 antidote_HigA addict 23.3 63 0.0014 23.9 2.0 23 148-170 21-43 (78)
177 PRK05572 sporulation sigma fac 23.1 1.5E+02 0.0033 27.2 5.0 49 121-177 202-250 (252)
178 PF13936 HTH_38: Helix-turn-he 22.7 98 0.0021 21.2 2.7 40 120-167 3-42 (44)
179 PRK09643 RNA polymerase sigma 22.5 2E+02 0.0044 25.1 5.4 49 121-177 134-182 (192)
180 PRK09638 RNA polymerase sigma 22.3 90 0.0019 26.5 3.0 48 122-177 127-174 (176)
181 TIGR02394 rpoS_proteo RNA poly 21.8 2.2E+02 0.0047 26.9 5.8 54 121-178 222-275 (285)
182 PRK05911 RNA polymerase sigma 21.5 1.8E+02 0.0039 27.1 5.1 49 121-177 205-253 (257)
183 PRK09636 RNA polymerase sigma 21.5 1.7E+02 0.0037 27.5 5.0 48 121-176 115-162 (293)
184 PHA00542 putative Cro-like pro 21.3 1.1E+02 0.0023 23.8 3.0 34 147-180 33-66 (82)
185 PRK08241 RNA polymerase factor 20.8 1.2E+02 0.0026 29.0 3.9 47 121-175 153-199 (339)
186 PF14644 DUF4456: Domain of un 20.6 2.2E+02 0.0047 26.0 5.3 56 15-70 36-91 (208)
187 TIGR02984 Sig-70_plancto1 RNA 20.4 1.7E+02 0.0038 24.8 4.5 48 121-176 140-187 (189)
188 PF14978 MRP-63: Mitochondrial 20.3 3.5E+02 0.0075 22.0 5.8 35 138-173 37-71 (91)
No 1
>PF07526 POX: Associated with HOX; InterPro: IPR006563 This domain in found exclusively in plant proteins, associated with HOX domains which may suggest these proteins are homeodomain transcription factors.
Probab=99.93 E-value=6.6e-27 Score=201.50 Aligned_cols=61 Identities=49% Similarity=0.781 Sum_probs=59.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccccHHHHHHHHHhhcccchHHHH
Q 040555 14 WHELQLLALKVYWKYKLYCQQMQSVVASFETVAGLGHAAPYISFAFKAISKHFCCLKNAIL 74 (313)
Q Consensus 14 ~~~l~~~l~ev~~ry~~y~~qmq~v~~sfe~~ag~g~a~~y~~lal~~~Sr~Fr~l~~~i~ 74 (313)
+.|||+||||||+||+|||+|||+||+|||+|||.|+|++||+||+++|||||||||++|.
T Consensus 79 K~KLl~mL~eVd~RY~qY~~Qmq~VvssFe~vaG~gaA~~YtalAlqamSrhFR~LRdaI~ 139 (140)
T PF07526_consen 79 KAKLLSMLDEVDRRYRQYYDQMQAVVSSFEAVAGLGAAAPYTALALQAMSRHFRCLRDAIS 139 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchhhHHHHHHHHHHHHHHHHHHhc
Confidence 3499999999999999999999999999999999999999999999999999999999996
No 2
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.93 E-value=9.4e-26 Score=210.49 Aligned_cols=115 Identities=25% Similarity=0.430 Sum_probs=109.1
Q ss_pred ccHHHHHHHHHhhcccchHHHHHHHHHhcccCccCcCCCCCCCCCCCCCCccccCCCC-CCCCCCCCCCC---CChhHHH
Q 040555 53 PYISFAFKAISKHFCCLKNAILDQIHVSGSKTVSDKNANNDTTEPGCSSHKPVQKLGF-LRPPHWRSQRA---LPDHAVA 128 (313)
Q Consensus 53 ~y~~lal~~~Sr~Fr~l~~~i~~ql~~~~~~~~~~~~~~~~~~~~l~~~dk~~q~~~~-l~~~~~r~rr~---lp~~a~~ 128 (313)
.|..|+-...++||..-.|..+|+||+.+.| .++++.++++||+|||||.+++| +|+++|++..+ |.++++.
T Consensus 114 nf~eLY~iLE~h~Fs~~~h~~LQ~lWl~AhY----~EAek~RGR~LgaV~KYRvRrKfPlPrTIWDGEet~yCFKekSR~ 189 (304)
T KOG0775|consen 114 NFRELYHILENHKFSPHNHPKLQALWLKAHY----KEAEKLRGRPLGAVDKYRVRRKFPLPRTIWDGEETVYCFKEKSRS 189 (304)
T ss_pred cHHHHHHHHHhccCChhhhHHHHHHHHHHHH----HHHHHhcCCcCCccccceeeccCCCCCccccCceeeeehhHhhHH
Confidence 4889999999999999999999999997777 56778888999999999999999 99999999876 9999999
Q ss_pred HHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhc
Q 040555 129 VLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLW 174 (313)
Q Consensus 129 iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~k 174 (313)
+|++||.. +|||++++|++||+.|||+..||+|||+|||+|.+
T Consensus 190 ~LrewY~~---~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 190 LLREWYLQ---NPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred HHHHHHhc---CCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 99999998 99999999999999999999999999999999987
No 3
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=99.93 E-value=2.5e-26 Score=220.92 Aligned_cols=173 Identities=39% Similarity=0.600 Sum_probs=140.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccccHHHHHHHHHhhcccchH--HHHHHHHHhcccCccCc--CCC
Q 040555 16 ELQLLALKVYWKYKLYCQQMQSVVASFETVAGLGHAAPYISFAFKAISKHFCCLKN--AILDQIHVSGSKTVSDK--NAN 91 (313)
Q Consensus 16 ~l~~~l~ev~~ry~~y~~qmq~v~~sfe~~ag~g~a~~y~~lal~~~Sr~Fr~l~~--~i~~ql~~~~~~~~~~~--~~~ 91 (313)
||+.||.+|+.+|.+|+..|+.|.+.|+.+.|.+.+..|+.+++..+++||+++++ +|..|+........... +..
T Consensus 124 k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~ 203 (342)
T KOG0773|consen 124 KLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSEELLGESEQDDSE 203 (342)
T ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhcccccccccccccccccccccccc
Confidence 89999999999999999999999999999999999999999999999999999998 67777776655421110 011
Q ss_pred CCC-----CCCCCCCCcc-ccC------CCCCCCCCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCCh
Q 040555 92 NDT-----TEPGCSSHKP-VQK------LGFLRPPHWRSQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSK 159 (313)
Q Consensus 92 ~~~-----~~~l~~~dk~-~q~------~~~l~~~~~r~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~ 159 (313)
... .++....+.. ++. .+......||++++||+.++.+|++|+++|+.||||++.+|..||++|||+.
T Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~ 283 (342)
T KOG0773|consen 204 DESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSR 283 (342)
T ss_pred cccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCc
Confidence 110 1111111111 111 1123356899999999999999999999999999999999999999999999
Q ss_pred HHHhhhhhhhHhhhchhhHHHHHhhhhcC
Q 040555 160 NQVSNWFINARVRLWKPMVEEVHMLEIGQ 188 (313)
Q Consensus 160 ~QV~NWF~N~R~R~kk~~~~e~~~~~~~~ 188 (313)
.||+|||+|+|+|.|++|+++.+......
T Consensus 284 ~Qv~NWFINaR~R~w~p~~~~~~~~~~~~ 312 (342)
T KOG0773|consen 284 PQVSNWFINARVRLWKPMIEEMYLLEDKD 312 (342)
T ss_pred ccCCchhhhcccccCCchHHHHHHHhhcc
Confidence 99999999999999999999999887764
No 4
>smart00574 POX domain associated with HOX domains.
Probab=99.91 E-value=3.2e-25 Score=189.69 Aligned_cols=64 Identities=48% Similarity=0.776 Sum_probs=60.6
Q ss_pred HHhHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccccHHHHHHHHHhhcccchHHHH
Q 040555 11 KLAWH--ELQLLALKVYWKYKLYCQQMQSVVASFETVAGLGHAAPYISFAFKAISKHFCCLKNAIL 74 (313)
Q Consensus 11 ~~~~~--~l~~~l~ev~~ry~~y~~qmq~v~~sfe~~ag~g~a~~y~~lal~~~Sr~Fr~l~~~i~ 74 (313)
+++|. ||++||||||+||+|||+|||+|+++||+|+|.|++++||+||+++||+||||||++|.
T Consensus 74 e~q~kk~kLl~mL~eVd~RY~qY~~qmq~v~ssFe~vaG~g~a~~yt~lAl~a~SrhFr~LrdaI~ 139 (140)
T smart00574 74 ELQRKKAKLLSMLEEVDRRYKHYYEQMQTVVSSFDQAAGLGAAKPYTALALKTISRHFRCLKDAIA 139 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHhc
Confidence 44554 89999999999999999999999999999999999999999999999999999999985
No 5
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=99.65 E-value=1.1e-16 Score=110.74 Aligned_cols=40 Identities=63% Similarity=1.133 Sum_probs=36.4
Q ss_pred HHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhh
Q 040555 133 WLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVR 172 (313)
Q Consensus 133 wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R 172 (313)
||.+|+.||||+.+||..||++|||+.+||+|||+|+|+|
T Consensus 1 Wl~~h~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 1 WLLEHLHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp HHHHTTTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CHHHHCCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 8999999999999999999999999999999999999997
No 6
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=99.60 E-value=6.2e-15 Score=137.73 Aligned_cols=65 Identities=37% Similarity=0.665 Sum_probs=62.1
Q ss_pred CCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHH
Q 040555 115 HWRSQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVE 179 (313)
Q Consensus 115 ~~r~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~ 179 (313)
++|+||+|++.++.+|..||..|+.||||++++|.+||++++++..||+|||.|.|.|.+|.+..
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k 252 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGK 252 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhh
Confidence 46888999999999999999999999999999999999999999999999999999999998854
No 7
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.47 E-value=1.3e-13 Score=99.44 Aligned_cols=57 Identities=30% Similarity=0.580 Sum_probs=52.8
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchh
Q 040555 117 RSQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKP 176 (313)
Q Consensus 117 r~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~ 176 (313)
+.+..+++.++.+|++||.. +|||+..++..||.+|||+..||.+||+|+|.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEK---NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 34567999999999999999 9999999999999999999999999999999998753
No 8
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.46 E-value=1.2e-13 Score=100.11 Aligned_cols=57 Identities=35% Similarity=0.655 Sum_probs=53.6
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhch
Q 040555 116 WRSQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWK 175 (313)
Q Consensus 116 ~r~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk 175 (313)
+|+++.|+.+++.+|+.+|.. +|||+.+++..||..+||+..||.+||+|+|.+.++
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQE---NPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH---SSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH---hccccccccccccccccccccccccCHHHhHHHhCc
Confidence 356778999999999999999 999999999999999999999999999999999864
No 9
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.44 E-value=3.1e-13 Score=97.03 Aligned_cols=54 Identities=28% Similarity=0.537 Sum_probs=50.2
Q ss_pred CCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhc
Q 040555 118 SQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLW 174 (313)
Q Consensus 118 ~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~k 174 (313)
.+..|+++++.+|++||.. ++||+.+++..||..+||+..||.+||+|+|.|.+
T Consensus 3 ~r~~~~~~~~~~L~~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 3 KRTSFTPEQLEELEKEFQK---NPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 3445999999999999999 99999999999999999999999999999999863
No 10
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.00 E-value=2.1e-10 Score=110.27 Aligned_cols=63 Identities=25% Similarity=0.322 Sum_probs=55.0
Q ss_pred CCCCCC-CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHHH
Q 040555 115 HWRSQR-ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVEE 180 (313)
Q Consensus 115 ~~r~rr-~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~e 180 (313)
..||+| -++|.|+..|+.-|+- |-|.|++-|.+|++.++||..||++||||||+|+||-..|.
T Consensus 234 ~~RKKRcPYTK~QtlELEkEFlf---N~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 234 RGRKKRCPYTKHQTLELEKEFLF---NMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred ccccccCCchHHHHHHHHHHHHH---HHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence 334444 4999999999999888 99999999999999999999999999999999998865444
No 11
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.96 E-value=3.6e-10 Score=108.62 Aligned_cols=65 Identities=22% Similarity=0.343 Sum_probs=57.7
Q ss_pred CCCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHHHHH
Q 040555 115 HWRSQRA-LPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVEEVH 182 (313)
Q Consensus 115 ~~r~rr~-lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~e~~ 182 (313)
.+||+|. |++.+|-.|+.-|.+ ..|.+-.||+.||..++||.+||++||||+|-|.|+.-+++..
T Consensus 152 ~kRKrRVLFSqAQV~ELERRFrq---QRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~ 217 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRFRQ---QRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKAL 217 (307)
T ss_pred cccccccccchhHHHHHHHHHHh---hhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhh
Confidence 3444454 999999999999999 9999999999999999999999999999999999987766543
No 12
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.94 E-value=1.7e-09 Score=96.76 Aligned_cols=63 Identities=24% Similarity=0.336 Sum_probs=57.2
Q ss_pred CCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHHH
Q 040555 115 HWRSQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVEE 180 (313)
Q Consensus 115 ~~r~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~e 180 (313)
.+|.|+.|+.++...|+..|.. +.|-.-.||..||+.++|+++||++||||||.|.|+.-.++
T Consensus 102 ~kr~RT~ft~~Ql~~LE~~F~~---~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 102 PKRIRTAFTPEQLLKLEHAFEG---NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCccccccCHHHHHHHHHHHhc---CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 4455666999999999999999 99999999999999999999999999999999998876554
No 13
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.94 E-value=6.3e-10 Score=104.81 Aligned_cols=60 Identities=23% Similarity=0.282 Sum_probs=55.5
Q ss_pred CCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 115 HWRSQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 115 ~~r~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.+|.|+.|+..++..|+.-|.- |.|.+...|.+||..++|++.||++||||||+|.||..
T Consensus 159 ~kR~RtayT~~QllELEkEFhf---N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~ 218 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHF---NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKEN 218 (261)
T ss_pred CCCCCcccchhhhhhhhhhhcc---ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhh
Confidence 4566667999999999999998 99999999999999999999999999999999998754
No 14
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.90 E-value=4.6e-09 Score=97.12 Aligned_cols=64 Identities=20% Similarity=0.290 Sum_probs=57.9
Q ss_pred CCCCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhH
Q 040555 112 RPPHWRSQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMV 178 (313)
Q Consensus 112 ~~~~~r~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~ 178 (313)
.+.++++|+-++.-+...|+.-|.+ +.|.--.||.+||..+|||.+||++||||||-|.||.+.
T Consensus 119 ~KK~RKPRTIYSS~QLqaL~rRFQk---TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 119 GKKVRKPRTIYSSLQLQALNRRFQQ---TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred cccccCCcccccHHHHHHHHHHHhh---cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 3455666777999999999999999 999999999999999999999999999999999988764
No 15
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.89 E-value=7.1e-09 Score=100.10 Aligned_cols=59 Identities=31% Similarity=0.478 Sum_probs=54.0
Q ss_pred CCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHH
Q 040555 118 SQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVE 179 (313)
Q Consensus 118 ~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~ 179 (313)
.|+.|+..++..|+.-|.. --|.+..||.+||..+|||..||..||||||.|+|+...+
T Consensus 175 sRTaFT~~Ql~~LEkrF~~---QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 175 SRTAFSDHQLFELEKRFEK---QKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred chhhhhHHHHHHHHHHHHH---hhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 3344999999999999999 9999999999999999999999999999999998877655
No 16
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.86 E-value=4.1e-09 Score=99.09 Aligned_cols=61 Identities=30% Similarity=0.467 Sum_probs=57.0
Q ss_pred CCCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchh
Q 040555 113 PPHWRSQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKP 176 (313)
Q Consensus 113 ~~~~r~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~ 176 (313)
...+|+|+-|+.++..-|++-|.+ |.|.++..|..||.++||.+.||+.||||+|.++||.
T Consensus 244 ~eeKRPRTAFtaeQL~RLK~EF~e---nRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 244 KEEKRPRTAFTAEQLQRLKAEFQE---NRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred chhcCccccccHHHHHHHHHHHhh---hhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 355777888999999999999999 9999999999999999999999999999999999874
No 17
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.85 E-value=2.9e-09 Score=96.93 Aligned_cols=67 Identities=27% Similarity=0.278 Sum_probs=60.1
Q ss_pred CCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHHHHHhh
Q 040555 115 HWRSQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVEEVHML 184 (313)
Q Consensus 115 ~~r~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~e~~~~ 184 (313)
.++++++|+.+++..|+.-|.. +-|-.+.+|..||+++||.+.||..||||||.|.|.+-.+.-+..
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~---~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~ 116 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFES---EKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYES 116 (198)
T ss_pred cccccccccHHHHHHhHHhhcc---ccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHH
Confidence 4677888999999999999999 889999999999999999999999999999999988776655443
No 18
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=98.78 E-value=9.8e-09 Score=76.55 Aligned_cols=52 Identities=8% Similarity=0.264 Sum_probs=48.9
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCC----CCHHHHHHHHHHhCCChHHHhhhhhhhH
Q 040555 116 WRSQRALPDHAVAVLKTWLYENFLHPY----PTDSDKQILAKQTGLSKNQVSNWFINAR 170 (313)
Q Consensus 116 ~r~rr~lp~~a~~iL~~wf~~h~~~PY----Ps~~eK~~LA~~tgLs~~QV~NWF~N~R 170 (313)
+|.|+.|+.+++..|+..|.. ++| |+..++..||..+||+..+|.+||+|-+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~---~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEK---LGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHH---cCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 567778999999999999999 999 9999999999999999999999999964
No 19
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.76 E-value=2.2e-08 Score=82.82 Aligned_cols=60 Identities=20% Similarity=0.334 Sum_probs=54.5
Q ss_pred CCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHHH
Q 040555 118 SQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVEE 180 (313)
Q Consensus 118 ~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~e 180 (313)
-+.+|+..+...|+..|.+ .-||+.-.|++||-...|++..|..||||+|.+.+|...-.
T Consensus 20 IRTTFTS~QLkELErvF~E---THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a 79 (125)
T KOG0484|consen 20 IRTTFTSAQLKELERVFAE---THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAA 79 (125)
T ss_pred hhhhhhHHHHHHHHHHHHh---hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHH
Confidence 3456999999999999999 99999999999999999999999999999999998865433
No 20
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.75 E-value=7.3e-09 Score=95.26 Aligned_cols=64 Identities=19% Similarity=0.284 Sum_probs=57.2
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHHH
Q 040555 114 PHWRSQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVEE 180 (313)
Q Consensus 114 ~~~r~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~e 180 (313)
.++|.|+.|+..+|..|+.-|.. ..|.+.+||..||+++.||++||+.||||+|.|.|+....+
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~---krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad 166 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFEL---KRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAAD 166 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHH---HhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhh
Confidence 44555666999999999999998 89999999999999999999999999999999998876444
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.73 E-value=1.3e-08 Score=89.60 Aligned_cols=61 Identities=25% Similarity=0.366 Sum_probs=56.0
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 114 PHWRSQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 114 ~~~r~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
...+++++.+..++.+|+..|.. +|||+..+|..|+..++++++-|..||||+|.+.++.-
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i---~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~ 110 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEI---NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKR 110 (156)
T ss_pred cCcccceechHHHHHHHHHHhcc---CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhc
Confidence 34566777999999999999999 99999999999999999999999999999999998754
No 22
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.64 E-value=1.9e-08 Score=94.91 Aligned_cols=56 Identities=32% Similarity=0.348 Sum_probs=52.2
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHHH
Q 040555 122 LPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVEE 180 (313)
Q Consensus 122 lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~e 180 (313)
++..++-.|+..|.- ++|.|...|.+||..+||++.||++||||||.|++|...+.
T Consensus 206 YTDhQRLELEKEfh~---SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 206 YTDHQRLELEKEFHT---SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ecchhhhhhhhhhcc---ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 899999999999998 99999999999999999999999999999999998765444
No 23
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.63 E-value=3.2e-08 Score=91.09 Aligned_cols=61 Identities=21% Similarity=0.382 Sum_probs=54.9
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 114 PHWRSQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 114 ~~~r~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
..+|-|++|+..+..+|++-|.+ ..||+...+++||.+++|.+.+|.+||+|+|.+.++.-
T Consensus 36 kqRRERTtFtr~QlevLe~LF~k---TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq 96 (228)
T KOG2251|consen 36 KQRRERTTFTRKQLEVLEALFAK---TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQ 96 (228)
T ss_pred hcccccceecHHHHHHHHHHHHh---hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhh
Confidence 33445556999999999999999 99999999999999999999999999999999987654
No 24
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.62 E-value=4.3e-08 Score=89.70 Aligned_cols=62 Identities=18% Similarity=0.340 Sum_probs=55.6
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhH
Q 040555 114 PHWRSQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMV 178 (313)
Q Consensus 114 ~~~r~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~ 178 (313)
+-+++|.-|+..+...|++-|.+ ..|.+.+||.+++.-+.||.+||++||||||.|.|+--.
T Consensus 143 ~nRkPRtPFTtqQLlaLErkfre---kqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe 204 (246)
T KOG0492|consen 143 PNRKPRTPFTTQQLLALERKFRE---KQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE 204 (246)
T ss_pred CCCCCCCCCCHHHHHHHHHHHhH---hhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence 34556666999999999999999 999999999999999999999999999999999877543
No 25
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.56 E-value=3.3e-08 Score=97.48 Aligned_cols=58 Identities=21% Similarity=0.355 Sum_probs=53.1
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchh
Q 040555 116 WRSQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKP 176 (313)
Q Consensus 116 ~r~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~ 176 (313)
+|+|+.+...++..|+..|.. ||.|+.+|.-.||++++|.+..|++||+|||+|+|+.
T Consensus 295 RKKRTSie~~vr~aLE~~F~~---npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~ 352 (398)
T KOG3802|consen 295 RKKRTSIEVNVRGALEKHFLK---NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRI 352 (398)
T ss_pred cccccceeHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhccccceEEEEeeccccccccC
Confidence 334445999999999999999 9999999999999999999999999999999999875
No 26
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.43 E-value=9.8e-08 Score=84.68 Aligned_cols=57 Identities=26% Similarity=0.411 Sum_probs=52.2
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhH
Q 040555 119 QRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMV 178 (313)
Q Consensus 119 rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~ 178 (313)
|..|+..+...|+.-|.. ..|.+-.|+.+||..++|+++||+.||||+|.+-||-..
T Consensus 104 Rtvfs~~ql~~l~~rFe~---QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r 160 (194)
T KOG0491|consen 104 RTVFSDPQLSGLEKRFER---QRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQR 160 (194)
T ss_pred cccccCccccccHHHHhh---hhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHh
Confidence 345999999999999998 899999999999999999999999999999999987653
No 27
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.40 E-value=2.9e-07 Score=86.78 Aligned_cols=55 Identities=24% Similarity=0.420 Sum_probs=51.4
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 120 RALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 120 r~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
+.|+..+...|+.-|.+ .-||+...|++||..|+|.+..|.+||||||.+++|..
T Consensus 146 TiFT~~Qle~LEkaFke---aHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~E 200 (332)
T KOG0494|consen 146 TIFTSYQLEELEKAFKE---AHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTE 200 (332)
T ss_pred chhhHHHHHHHHHHHhh---ccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhh
Confidence 34999999999999999 99999999999999999999999999999999987653
No 28
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.38 E-value=2.5e-07 Score=89.07 Aligned_cols=59 Identities=22% Similarity=0.348 Sum_probs=53.5
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHHHH
Q 040555 120 RALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVEEV 181 (313)
Q Consensus 120 r~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~e~ 181 (313)
..|.-.+...|+.||.. |.||+.+.|++||-=|+||+..|++||+|+|.+++|....+.
T Consensus 117 thFtSqqlqele~tF~r---NrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 117 THFTSQQLQELEATFQR---NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhHHHHHHHHHHHHhh---ccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 34999999999999999 999999999999999999999999999999999877654443
No 29
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.28 E-value=5.4e-07 Score=86.04 Aligned_cols=61 Identities=23% Similarity=0.385 Sum_probs=56.5
Q ss_pred CCCCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhch
Q 040555 112 RPPHWRSQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWK 175 (313)
Q Consensus 112 ~~~~~r~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk 175 (313)
..+.+|+|++++.++...|+..|.. .|.|-.--|++|+..|||....|+.||||||.++|+
T Consensus 164 d~~nKRPRTTItAKqLETLK~AYn~---SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKR 224 (383)
T KOG4577|consen 164 DASNKRPRTTITAKQLETLKQAYNT---SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKR 224 (383)
T ss_pred ccccCCCcceeeHHHHHHHHHHhcC---CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHh
Confidence 3467899999999999999999998 999999999999999999999999999999987754
No 30
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.27 E-value=1.6e-06 Score=88.59 Aligned_cols=56 Identities=23% Similarity=0.336 Sum_probs=52.8
Q ss_pred CCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhh
Q 040555 115 HWRSQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRL 173 (313)
Q Consensus 115 ~~r~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~ 173 (313)
.+|+|-.|+..+++.|++.|.+ +++|+.+.-+.|+.+++|..+-|.|||-|+|+|.
T Consensus 420 ~KKPRlVfTd~QkrTL~aiFke---~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 420 TKKPRLVFTDIQKRTLQAIFKE---NKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred CCCceeeecHHHHHHHHHHHhc---CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 3566777999999999999999 9999999999999999999999999999999996
No 31
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=98.14 E-value=2.3e-06 Score=79.17 Aligned_cols=62 Identities=23% Similarity=0.384 Sum_probs=55.5
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHHHHHhh
Q 040555 120 RALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVEEVHML 184 (313)
Q Consensus 120 r~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~e~~~~ 184 (313)
.+|...++-.|+.-|.+ ..||--.++-+||...|+++.||.+||||||.+++|.-.-|+...
T Consensus 172 PTf~g~qi~~le~~feq---tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmasa 233 (288)
T KOG0847|consen 172 PTFTGHQIYQLERKFEQ---TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMASA 233 (288)
T ss_pred CCccchhhhhhhhhhhh---hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhhc
Confidence 45999999999999999 999999999999999999999999999999999988766665433
No 32
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=98.00 E-value=2.1e-06 Score=82.68 Aligned_cols=62 Identities=21% Similarity=0.342 Sum_probs=54.7
Q ss_pred CCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHH
Q 040555 115 HWRSQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVE 179 (313)
Q Consensus 115 ~~r~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~ 179 (313)
.+|=|+-|+.+++.-|++-|.+ --|-+...|.+||.+++|.++.|+.||||||.|.|+..+.
T Consensus 181 mRRYRTAFTReQIaRLEKEFyr---ENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEFYR---ENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHHHH---hccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 3444555999999999888887 7899999999999999999999999999999999987764
No 33
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.79 E-value=3.1e-05 Score=76.25 Aligned_cols=63 Identities=25% Similarity=0.462 Sum_probs=56.1
Q ss_pred CCCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhH
Q 040555 113 PPHWRSQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMV 178 (313)
Q Consensus 113 ~~~~r~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~ 178 (313)
+...|.++.|+..+...|+.+|.. ++||....++.||.+++|+...|..||.|+|.|.++...
T Consensus 174 ~~~rr~rtsft~~Q~~~le~~f~r---t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 174 RGGRRNRTSFSPSQLEALEECFQR---TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred ccccccccccccchHHHHHHHhcC---CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 344455567999999999999999 899999999999999999999999999999999887653
No 34
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.69 E-value=1.8e-05 Score=71.15 Aligned_cols=61 Identities=16% Similarity=0.110 Sum_probs=54.5
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 114 PHWRSQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 114 ~~~r~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
..+|.+.+|+..+.+.|+.-|.. ++||+...++.||..+++++..|.+||+|+|.+.++..
T Consensus 59 ~~rr~rt~~~~~ql~~ler~f~~---~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 59 SKRCARCKFTISQLDELERAFEK---VHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred cccccCCCCCcCHHHHHHHhhcC---CCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 34555667999999999999999 79999999999999999999999999999999987643
No 35
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.30 E-value=7.1e-05 Score=71.89 Aligned_cols=59 Identities=22% Similarity=0.387 Sum_probs=51.6
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhch
Q 040555 114 PHWRSQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWK 175 (313)
Q Consensus 114 ~~~r~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk 175 (313)
.++|+|+.+-...++.|++||.. .|-|+.+....+|+.++|....|..||+|.|++-|+
T Consensus 308 ekKRKRTSIAAPEKRsLEayFav---QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAV---QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred ccccccccccCcccccHHHHhcc---CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence 34555555666667889999999 999999999999999999999999999999999876
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.18 E-value=0.00019 Score=69.57 Aligned_cols=59 Identities=44% Similarity=0.674 Sum_probs=53.7
Q ss_pred CCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 118 SQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 118 ~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
++.+++.++ ..|+.|+.+|-.++||+.-++..|+-.++++..||++||.|+|+|+++.+
T Consensus 98 ~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~ 156 (342)
T KOG0773|consen 98 RRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKEL 156 (342)
T ss_pred ccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhcc
Confidence 344578888 99999999999999999999999999999999999999999999987654
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.91 E-value=0.00089 Score=49.79 Aligned_cols=43 Identities=21% Similarity=0.414 Sum_probs=31.5
Q ss_pred HHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhh
Q 040555 127 VAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVR 172 (313)
Q Consensus 127 ~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R 172 (313)
.+.|+++|.. |.++...+-..|+.+++|+..||.+||.-++.+
T Consensus 10 ~~pL~~Yy~~---h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLK---HKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHH---T----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHH---cCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 4559999999 899999999999999999999999999877554
No 38
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=96.61 E-value=0.0029 Score=56.85 Aligned_cols=62 Identities=31% Similarity=0.530 Sum_probs=54.9
Q ss_pred CCCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 113 PPHWRSQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 113 ~~~~r~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
....+.+..+...+...+...|.. .+||+...+..|+..+|++...|.+||+|.|.+.++..
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~---~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFRA---TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred cccCCCccccccchhHhhhhcccC---CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 344556667999999999999988 99999999999999999999999999999999997654
No 39
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=93.36 E-value=0.06 Score=60.67 Aligned_cols=56 Identities=25% Similarity=0.402 Sum_probs=52.3
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhH
Q 040555 120 RALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMV 178 (313)
Q Consensus 120 r~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~ 178 (313)
..+...++.++++.|.. .-||+.++-+.|.+..+|....|..||+|+|.+.+|+..
T Consensus 908 ~~~~d~qlk~i~~~~~~---q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 908 TQESDLQLKIIKACYEA---QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred cchhHHHHHHHHHHHhh---ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 34888899999999999 999999999999999999999999999999999998865
No 40
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=86.12 E-value=1.3 Score=47.96 Aligned_cols=44 Identities=23% Similarity=0.436 Sum_probs=41.6
Q ss_pred HHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhh
Q 040555 127 VAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRL 173 (313)
Q Consensus 127 ~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~ 173 (313)
..+|+++|.. |+.|+.++-..+|.+.||...-|+.||.+.+...
T Consensus 568 ~sllkayyal---n~~ps~eelskia~qvglp~~vvk~wfE~~~a~e 611 (1007)
T KOG3623|consen 568 TSLLKAYYAL---NGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEE 611 (1007)
T ss_pred HHHHHHHHHh---cCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhh
Confidence 6889999999 9999999999999999999999999999998765
No 41
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=84.56 E-value=2.1 Score=30.96 Aligned_cols=46 Identities=24% Similarity=0.279 Sum_probs=30.4
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhH
Q 040555 117 RSQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINAR 170 (313)
Q Consensus 117 r~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R 170 (313)
|+++.|+-+..-.+-..+.. .+ -...+|+..|++.++|++|..|+.
T Consensus 2 rkR~~LTl~eK~~iI~~~e~---g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 2 RKRKSLTLEEKLEIIKRLEE---GE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSS--HHHHHHHHHHHHC---TT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCccCCHHHHHHHHHHHHc---CC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 56667887775444444554 33 588999999999999999999954
No 42
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=75.75 E-value=8.3 Score=25.47 Aligned_cols=45 Identities=22% Similarity=0.268 Sum_probs=35.2
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhc
Q 040555 122 LPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLW 174 (313)
Q Consensus 122 lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~k 174 (313)
+++....++...+.+ -+ .-..+|..+|++...|..|....+.+++
T Consensus 11 l~~~~~~~~~~~~~~----~~----~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 11 LPEREREVILLRFGE----GL----SYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred CCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 677788888777654 22 3567899999999999999988887653
No 43
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=74.02 E-value=6.8 Score=27.23 Aligned_cols=47 Identities=23% Similarity=0.355 Sum_probs=37.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhch
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWK 175 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk 175 (313)
.||++...++...|++ .+ .-.++|+.+|+|...|+.+...+..++++
T Consensus 4 ~L~~~er~vi~~~y~~----~~----t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE----GL----TLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHTS----T-----SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC----CC----CHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 4889999999888854 32 35789999999999999999999888753
No 44
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=72.97 E-value=7.3 Score=27.28 Aligned_cols=45 Identities=20% Similarity=0.329 Sum_probs=33.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRL 173 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~ 173 (313)
.+|+....++...|.+ .+ .-.++|+.+|+|...|.+|...+|+++
T Consensus 10 ~L~~~~r~i~~l~~~~----g~----s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQ----GM----SYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp CS-HHHHHHHHHHHTS-----------HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHH----Cc----CHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 3788888888776664 22 457899999999999999999998764
No 45
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=68.05 E-value=15 Score=26.30 Aligned_cols=37 Identities=24% Similarity=0.310 Sum_probs=23.4
Q ss_pred HHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhh
Q 040555 130 LKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRL 173 (313)
Q Consensus 130 L~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~ 173 (313)
|+.++.+ +.+ ....||+.+|++..+|+.|+.+...+.
T Consensus 2 L~~~m~~---~~i----t~~~La~~~gis~~tl~~~~~~~~~~~ 38 (63)
T PF13443_consen 2 LKELMAE---RGI----TQKDLARKTGISRSTLSRILNGKPSNP 38 (63)
T ss_dssp HHHHHHH---TT------HHHHHHHHT--HHHHHHHHTTT----
T ss_pred HHHHHHH---cCC----CHHHHHHHHCcCHHHHHHHHhcccccc
Confidence 4555565 343 567899999999999999999874443
No 46
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=67.71 E-value=9.4 Score=32.15 Aligned_cols=51 Identities=24% Similarity=0.196 Sum_probs=40.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHH
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVE 179 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~ 179 (313)
.||+..+.++...+.+. .+ -.++|+.+|++...|.+.+.-+|.++++.+.+
T Consensus 106 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (160)
T PRK09642 106 ELPENYRDVVLAHYLEE--KS------YQEIALQEKIEVKTVEMKLYRARKWIKKHWKE 156 (160)
T ss_pred hCCHHHHHHHHHHHHhC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 38998888887766652 22 35899999999999999999999999876643
No 47
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=66.35 E-value=9.9 Score=28.21 Aligned_cols=46 Identities=20% Similarity=0.338 Sum_probs=29.8
Q ss_pred CCCCCCChhHHH-HHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhH
Q 040555 117 RSQRALPDHAVA-VLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINAR 170 (313)
Q Consensus 117 r~rr~lp~~a~~-iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R 170 (313)
++++.|+++.+. ++...+.. ......+|+..|+++.+|.+|-.-.+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~--------g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES--------GESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH--------HCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC--------CCceEeeecccccccccccHHHHHHh
Confidence 345678888864 44444343 35788999999999999999987666
No 48
>KOG0809 consensus SNARE protein TLG2/Syntaxin 16 [Intracellular trafficking, secretion, and vesicular transport]
Probab=66.06 E-value=13 Score=36.35 Aligned_cols=77 Identities=17% Similarity=0.236 Sum_probs=64.9
Q ss_pred chhhccHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHhcCCCccccHHHHHHHHHhhcccchHHHHHHHHH
Q 040555 5 ASYVSSKLAWHELQLLALKVYWKYKLYCQQMQSVVASF-----ETVAGLGHAAPYISFAFKAISKHFCCLKNAILDQIHV 79 (313)
Q Consensus 5 ~~~~~~~~~~~~l~~~l~ev~~ry~~y~~qmq~v~~sf-----e~~ag~g~a~~y~~lal~~~Sr~Fr~l~~~i~~ql~~ 79 (313)
.+|=.....-+....+.++|-+-..+|...||.+-++. +...+...+..|-++.++++|.-||-+....+..|..
T Consensus 90 PsF~Dk~ede~~IE~ltq~Itqll~~cqk~iq~~~a~~n~~~~~e~~~~~n~~~~la~~LQ~~s~~fR~~Qs~YLK~l~~ 169 (305)
T KOG0809|consen 90 PSFSDKREDEHEIEELTQEITQLLQKCQKLIQRLSASLNQLSPSERLLRKNAQGYLALQLQTLSREFRGLQSKYLKRLRN 169 (305)
T ss_pred CCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 35556666667888999999999999999999999888 5556666777899999999999999999999999887
Q ss_pred hc
Q 040555 80 SG 81 (313)
Q Consensus 80 ~~ 81 (313)
--
T Consensus 170 ~e 171 (305)
T KOG0809|consen 170 RE 171 (305)
T ss_pred hh
Confidence 33
No 49
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=63.69 E-value=23 Score=20.64 Aligned_cols=38 Identities=13% Similarity=0.239 Sum_probs=27.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWF 166 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF 166 (313)
.++.+....+...+.. .+ ....+|+.+|++...|.+|.
T Consensus 5 ~~~~~~~~~i~~~~~~----~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAA----GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHhC
Confidence 3666666656555543 33 45688999999999999984
No 50
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=60.40 E-value=19 Score=29.91 Aligned_cols=47 Identities=13% Similarity=0.118 Sum_probs=38.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhch
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWK 175 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk 175 (313)
.||+..+.++...|.+. + .-.++|+.+|++...|.+|...+|.++++
T Consensus 106 ~L~~~~r~ii~l~~~~~----~----s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG----K----TMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 48999999887666652 2 35789999999999999999999998865
No 51
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=59.78 E-value=23 Score=31.13 Aligned_cols=53 Identities=15% Similarity=0.238 Sum_probs=42.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHHHH
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVEEV 181 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~e~ 181 (313)
.||+..+.++.-.+.+ .+ .-.++|..+|+++..|.++..-+|.++++-+....
T Consensus 134 ~Lp~~~R~v~~L~~~~----g~----s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~ 186 (189)
T PRK12530 134 HLPAQQARVFMMREYL----EL----SSEQICQECDISTSNLHVLLYRARLQLQACLSKNW 186 (189)
T ss_pred hCCHHHHHHHhHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3888888888776664 22 34789999999999999999999999988775544
No 52
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=58.59 E-value=22 Score=29.27 Aligned_cols=48 Identities=21% Similarity=0.241 Sum_probs=38.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKP 176 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~ 176 (313)
.||+....++...+.+ .+ .-.++|+.+|++...|.++...+|.++++.
T Consensus 113 ~L~~~~r~il~l~~~~----~~----~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~ 160 (161)
T TIGR02985 113 KLPEQCRKIFILSRFE----GK----SYKEIAEELGISVKTVEYHISKALKELRKE 160 (161)
T ss_pred HCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 4888888888775554 33 335699999999999999999999988753
No 53
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=58.38 E-value=18 Score=31.21 Aligned_cols=49 Identities=16% Similarity=0.119 Sum_probs=40.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++...+.+. . .-.++|+.+|++...|.+++..+|.++++.+
T Consensus 131 ~L~~~~r~v~~l~~~~g--~------s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG--A------SIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 48999999998876652 2 3478999999999999999999999997665
No 54
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=57.71 E-value=24 Score=29.88 Aligned_cols=50 Identities=16% Similarity=0.088 Sum_probs=40.8
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 120 RALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 120 r~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
..||+..+.++.-.+.++ . .-.++|..+|++...|.+|..-+|.++++-+
T Consensus 107 ~~L~~~~r~v~~l~~~~g--~------s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE--L------TYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred HhCCHHHHHHHHhHHHhc--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 348999999998776653 2 3478999999999999999999999987654
No 55
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=57.11 E-value=17 Score=31.22 Aligned_cols=49 Identities=16% Similarity=0.149 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++.-.|.+ .+ .-.++|+.+|++...|.++...+|.++++.+
T Consensus 138 ~L~~~~r~v~~l~~~~----~~----s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 138 ALPEDLRTAITLRELE----GL----SYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCHHHhhhhhhhhhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3788888887765554 22 3478999999999999999999999987654
No 56
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=56.17 E-value=23 Score=28.12 Aligned_cols=48 Identities=25% Similarity=0.278 Sum_probs=37.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKP 176 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~ 176 (313)
.||+....++...+.. .+ .-.++|+.+|+++..|.+|....+.++++.
T Consensus 110 ~L~~~~~~ii~~~~~~----g~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~ 157 (158)
T TIGR02937 110 KLPEREREVLVLRYLE----GL----SYKEIAEILGISVGTVKRRLKRARKKLREL 157 (158)
T ss_pred hCCHHHHHHHhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 4778888877554443 33 446899999999999999999999888653
No 57
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=56.12 E-value=28 Score=29.23 Aligned_cols=49 Identities=20% Similarity=0.164 Sum_probs=39.2
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhH
Q 040555 122 LPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMV 178 (313)
Q Consensus 122 lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~ 178 (313)
||+..+.++...+.+ .+ .-.++|+.+|++...|.+|..-+|.++++.+.
T Consensus 126 L~~~~r~i~~l~~~~----~~----~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~ 174 (179)
T PRK11924 126 LPVKQREVFLLRYVE----GL----SYREIAEILGVPVGTVKSRLRRARQLLRECLE 174 (179)
T ss_pred CCHHHHHHhhHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 788888887665554 22 34789999999999999999999999987654
No 58
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=55.58 E-value=24 Score=30.96 Aligned_cols=49 Identities=16% Similarity=0.192 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++...+.+. + .-.++|+.+|++...|.+++..+|.++++.+
T Consensus 142 ~L~~~~r~vl~l~~~~~----~----s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG----L----TYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 48999999987766652 2 3478999999999999999999999987654
No 59
>PRK00118 putative DNA-binding protein; Validated
Probab=55.00 E-value=29 Score=28.85 Aligned_cols=48 Identities=13% Similarity=0.147 Sum_probs=39.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKP 176 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~ 176 (313)
.+|+.++.++..++.+ .+ .-.++|+.+|+++.-|.+|...+|.++++-
T Consensus 17 ~L~ekqRevl~L~y~e----g~----S~~EIAe~lGIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 17 LLTEKQRNYMELYYLD----DY----SLGEIAEEFNVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred cCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4788899999887775 22 345699999999999999999999988653
No 60
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=54.71 E-value=25 Score=31.30 Aligned_cols=49 Identities=22% Similarity=0.285 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++...+++. + .-.++|+.+|++...|.+++..+|.++++.+
T Consensus 153 ~L~~~~r~vl~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE----L----SQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 38889988887666542 2 3478999999999999999999999987655
No 61
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=54.34 E-value=31 Score=29.05 Aligned_cols=49 Identities=18% Similarity=0.209 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.|++..+.++...+.. .+ .-.++|+.+|++...|.+|...+++++++.+
T Consensus 128 ~L~~~~r~vl~l~~~~----~~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREIE----GL----SYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3888888888765554 22 2358999999999999999999999998755
No 62
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=53.85 E-value=20 Score=30.66 Aligned_cols=49 Identities=20% Similarity=0.180 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++...+.+ .+ .-.++|+.+|++...|.+++..+|+++++.+
T Consensus 136 ~L~~~~r~v~~l~~~~----g~----s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME----DL----SLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHhHHhhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 4888888888764443 22 3478999999999999999999999987643
No 63
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=53.20 E-value=29 Score=29.78 Aligned_cols=48 Identities=17% Similarity=0.272 Sum_probs=39.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKP 176 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~ 176 (313)
.||+....++...|.+ .+ .-.++|+.+|++...|.+++..+|.++++-
T Consensus 129 ~L~~~~r~i~~l~~~~----g~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 129 ELEKDRAAAVRRAYLE----GL----SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 3888888888877765 33 247899999999999999999999998764
No 64
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=52.75 E-value=35 Score=29.69 Aligned_cols=52 Identities=13% Similarity=0.141 Sum_probs=41.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHHH
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVEE 180 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~e 180 (313)
.||+.++.++.-.+.+. .+ -.++|..+|++..-|.+....+|.++++-+..+
T Consensus 131 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 182 (191)
T PRK12520 131 RLPPRTGRVFMMREWLE--LE------TEEICQELQITATNAWVLLYRARMRLRECLDLH 182 (191)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 38999988887776652 22 368999999999999999999999997765444
No 65
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=52.74 E-value=23 Score=31.14 Aligned_cols=51 Identities=24% Similarity=0.236 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHH
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVE 179 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~ 179 (313)
.||+....++.-.+.+. -+ -.++|+.+|++...|.+-+..+|+++++.+-+
T Consensus 141 ~Lp~~~r~v~~l~~~eg--~s------~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~~ 191 (194)
T PRK12531 141 RLPKAQRDVLQAVYLEE--LP------HQQVAEMFDIPLGTVKSRLRLAVEKLRHSMDA 191 (194)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHhCcCHHHHHHHHHHHHHHHHHHhhh
Confidence 48999999988766552 22 36899999999999999999999998775533
No 66
>PRK06930 positive control sigma-like factor; Validated
Probab=52.48 E-value=31 Score=30.63 Aligned_cols=55 Identities=13% Similarity=0.085 Sum_probs=43.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHHHHHh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVEEVHM 183 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~e~~~ 183 (313)
.||+..+.++.-.|.+ .+ .-.++|..+|++...|.++...+|.++++.+.++.+|
T Consensus 114 ~L~~rer~V~~L~~~e----g~----s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~l~~ 168 (170)
T PRK06930 114 VLTEREKEVYLMHRGY----GL----SYSEIADYLNIKKSTVQSMIERAEKKIARQINESLFC 168 (170)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 3888888888775554 22 3368999999999999999999999998877666544
No 67
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=51.90 E-value=24 Score=30.03 Aligned_cols=49 Identities=14% Similarity=0.079 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++.-.+.+. + .-.++|+.+|++...|.++..-+|.++++.+
T Consensus 112 ~L~~~~r~v~~l~~~~g----~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 112 LLSADQREAIILIGASG----F----SYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999888776652 2 3468999999999999999999999987543
No 68
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=51.35 E-value=33 Score=29.79 Aligned_cols=49 Identities=18% Similarity=0.147 Sum_probs=40.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++...|.+ .+ .-.++|+.+|++...|.++...+|.++++.+
T Consensus 139 ~L~~~~r~i~~l~~~~----g~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 187 (189)
T PRK09648 139 TLPEKQREILILRVVV----GL----SAEETAEAVGSTPGAVRVAQHRALARLRAEI 187 (189)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 4899999998876665 22 3578999999999999999999999987653
No 69
>PF13518 HTH_28: Helix-turn-helix domain
Probab=51.33 E-value=18 Score=24.68 Aligned_cols=25 Identities=24% Similarity=0.481 Sum_probs=21.3
Q ss_pred HHHHHHHHhCCChHHHhhhhhhhHh
Q 040555 147 DKQILAKQTGLSKNQVSNWFINARV 171 (313)
Q Consensus 147 eK~~LA~~tgLs~~QV~NWF~N~R~ 171 (313)
....+|+..|++..+|.+|.+..+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 3456999999999999999987765
No 70
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=50.84 E-value=28 Score=32.13 Aligned_cols=49 Identities=20% Similarity=0.273 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.+|...|.+. + .-.++|+.+|++...|.+|...++.++++.+
T Consensus 205 ~L~~~~r~vl~l~~~~g----~----s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l 253 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN----L----SQKETGERLGISQMHVSRLQRQAIKKLREAA 253 (257)
T ss_pred hCCHHHHHHHHHHHhCC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 48888888888776652 2 2378999999999999999999999987644
No 71
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=50.72 E-value=61 Score=21.65 Aligned_cols=47 Identities=21% Similarity=0.240 Sum_probs=35.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKP 176 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~ 176 (313)
.|++....++..+ .. .+ ...++|+.+|++...|..|....+.++.-.
T Consensus 3 ~l~~~e~~i~~~~-~~----g~----s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 3 SLTPREREVLRLL-AE----GL----TNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCCHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 4777778877543 32 22 457899999999999999999887777533
No 72
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=50.63 E-value=31 Score=30.01 Aligned_cols=49 Identities=22% Similarity=0.312 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||++...++...+++ .+ .-.++|+.+|++...|.+|+..+|.++++.+
T Consensus 141 ~L~~~~~~v~~l~~~~----g~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 141 QLPESQRQVLELAYYE----GL----SQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred hCCHHHhhhhhhhhhc----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788888888665554 22 3478999999999999999999999998755
No 73
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=50.52 E-value=40 Score=29.31 Aligned_cols=49 Identities=14% Similarity=0.226 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.+|.-.+.+ .+ .-.++|+.+|++...|.+-+..+|.++++.+
T Consensus 131 ~L~~~~r~vl~l~~~~----~~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 131 KLSPAHREIIDLVYYH----EK----SVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4899999988776654 22 3478999999999999999999999987754
No 74
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=49.72 E-value=31 Score=32.11 Aligned_cols=53 Identities=19% Similarity=0.335 Sum_probs=43.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHHHH
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVEEV 181 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~e~ 181 (313)
.||+..+.++.-.+.+. + .-.++|..+|++...|.++...+|.++++.+..+.
T Consensus 161 ~Lp~~~R~v~~L~~~eg----~----S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~ 213 (244)
T TIGR03001 161 ALSERERHLLRLHFVDG----L----SMDRIGAMYQVHRSTVSRWVAQARERLLERTRRRL 213 (244)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 48998888887777763 2 24689999999999999999999999988775554
No 75
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=49.47 E-value=30 Score=30.21 Aligned_cols=49 Identities=18% Similarity=0.239 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++.-.|.+. . .-.++|+.+|++...|.+...-+|.++++..
T Consensus 131 ~L~~~~r~i~~l~~~~g--~------s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG--E------KIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred hCCHHHHHHHHHHHHcc--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 48999999998766542 2 3478999999999999999999999987754
No 76
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=49.19 E-value=27 Score=29.29 Aligned_cols=49 Identities=27% Similarity=0.335 Sum_probs=39.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++...|.+ .+ .-.++|..+|++...|.++...+|.++++.+
T Consensus 110 ~L~~~~r~i~~l~~~~----g~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 110 RLPARQRAVVVLRYYE----DL----SEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred hCCHHHHHHhhhHHHh----cC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 4888888888776654 33 3467999999999999999999999987643
No 77
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=48.87 E-value=25 Score=29.59 Aligned_cols=47 Identities=26% Similarity=0.200 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhch
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWK 175 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk 175 (313)
.||+.++.++.-.+.+. + .-.++|..+|++...|..+...+|.++++
T Consensus 112 ~L~~~~r~v~~l~~~~~----~----s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 112 SLPLERRNVLLLRDYYG----F----SYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HCCHHHHHHhhhHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 48999988887766652 2 23689999999999999999999999865
No 78
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=48.82 E-value=24 Score=30.83 Aligned_cols=51 Identities=24% Similarity=0.184 Sum_probs=40.7
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHH
Q 040555 120 RALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVE 179 (313)
Q Consensus 120 r~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~ 179 (313)
..|++.++.+|+. +.+ .+ .-.++|+.+|++...|++|..+++.++++-...
T Consensus 5 ~~Lt~rqreVL~l-r~~----Gl----Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 5 SFLTERQIEVLRL-RER----GL----TQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred cCCCHHHHHHHHH-HHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 3589999999977 333 33 456899999999999999999999998766543
No 79
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=48.69 E-value=34 Score=29.59 Aligned_cols=48 Identities=15% Similarity=0.207 Sum_probs=38.6
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 122 LPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 122 lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
||+..+.++...|++ .+ .-.++|+.+|++...|.++...+|.++++.+
T Consensus 129 L~~~~r~i~~l~~~~----g~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 129 LPERQREAIVLQYYQ----GL----SNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred CCHHHHHHhhHHHhc----CC----CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 788888888665554 22 3468999999999999999999999987755
No 80
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=48.65 E-value=39 Score=28.97 Aligned_cols=47 Identities=17% Similarity=0.163 Sum_probs=39.3
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchh
Q 040555 122 LPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKP 176 (313)
Q Consensus 122 lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~ 176 (313)
||+.++.++.-.+.+ .+ .-.++|+.+|++...|.+.+..+|.++++.
T Consensus 135 Lp~~~r~v~~l~~~~----g~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 135 VDPRQAEVVELRFFA----GL----TVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CCHHHHHHHHHHHHc----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 899999998887765 22 346899999999999999999999998764
No 81
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=48.43 E-value=37 Score=28.23 Aligned_cols=47 Identities=28% Similarity=0.291 Sum_probs=38.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhch
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWK 175 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk 175 (313)
.||+....++...+.+ .+ .-.++|+.+|++...|.++...+|.++++
T Consensus 111 ~L~~~~r~v~~l~~~~----g~----~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 111 KLPERQRELLQLRYQR----GV----SLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HCCHHHHHHHHHHHhc----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 4899999988885554 33 34689999999999999999988888764
No 82
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=48.13 E-value=45 Score=29.95 Aligned_cols=53 Identities=17% Similarity=0.245 Sum_probs=42.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHHHH
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVEEV 181 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~e~ 181 (313)
.||+..+.++.--+.+. + .-.++|+.+|++...|.+...-+|+++++.+....
T Consensus 148 ~L~~~~r~v~~L~~~~g----~----s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~~ 200 (206)
T PRK12544 148 GLPAKYARVFMMREFIE----L----ETNEICHAVDLSVSNLNVLLYRARLRLRECLENKW 200 (206)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 48888888877666652 2 23789999999999999999999999988775543
No 83
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=47.66 E-value=31 Score=29.85 Aligned_cols=48 Identities=23% Similarity=0.142 Sum_probs=38.5
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 122 LPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 122 lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
||+....++.-.+.+. + .-.++|+.+|++...|.+.+..+|.++++.+
T Consensus 130 L~~~~r~v~~l~~~~g----~----s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 130 LPDRQRLPIVHVKLEG----L----SVAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred CCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 7888887776655542 2 3478999999999999999999999998755
No 84
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=47.35 E-value=31 Score=31.83 Aligned_cols=49 Identities=18% Similarity=0.226 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++...|.+. + .-.++|+.+|++...|+.+...++.++++.+
T Consensus 205 ~L~~~~r~ii~l~~~~g----~----s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN----L----SQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred cCCHHHHHHHHHHHcCC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 48888888888777653 2 2368999999999999999999999987644
No 85
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=46.98 E-value=55 Score=23.94 Aligned_cols=46 Identities=26% Similarity=0.344 Sum_probs=35.7
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhh
Q 040555 122 LPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFIN 168 (313)
Q Consensus 122 lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N 168 (313)
|++.+..+|+..+..=+.+ +|-...-.+||+.+|++..-|+.=+-+
T Consensus 1 LT~~Q~e~L~~A~~~GYfd-~PR~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFD-VPRRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred CCHHHHHHHHHHHHcCCCC-CCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 5778889998877653333 388889999999999999998764433
No 86
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=46.58 E-value=49 Score=27.53 Aligned_cols=50 Identities=22% Similarity=0.209 Sum_probs=40.4
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 120 RALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 120 r~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
..||+..+.++.-.+.+ .+ .-.++|+.+|++...|.+...-+|.++++.+
T Consensus 105 ~~Lp~~~r~v~~l~~~~----g~----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 105 QKLPARQREAFLLRYWE----DM----DVAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred HhCCHHHHHHHHHHHHh----cC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34899999988776665 22 2478999999999999999999999987655
No 87
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=46.54 E-value=46 Score=27.94 Aligned_cols=48 Identities=17% Similarity=0.266 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+....+|.-.+ + .+ .-.++|..+|++...|.++...+|.++++-+
T Consensus 112 ~L~~~~r~il~l~~-~----g~----s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 112 KMTERDRTVLLLRF-S----GY----SYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred cCCHHHHHHHHHHH-c----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48888888887766 5 22 3478999999999999999999999987755
No 88
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=46.25 E-value=34 Score=29.88 Aligned_cols=50 Identities=16% Similarity=0.216 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhH
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMV 178 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~ 178 (313)
.||+..+.++.-.+.+ .+ .-.++|+.+|++...|.++...+|.++++.+.
T Consensus 136 ~L~~~~r~i~~L~~~~----g~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 185 (195)
T PRK12532 136 NLPENTARVFTLKEIL----GF----SSDEIQQMCGISTSNYHTIMHRARESLRQCLQ 185 (195)
T ss_pred hCCHHHHHHhhhHHHh----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4888888888765554 22 34789999999999999999999999987663
No 89
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=45.85 E-value=26 Score=31.90 Aligned_cols=49 Identities=24% Similarity=0.331 Sum_probs=39.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++...|.+ .+ .-.++|+.+|++...|.++...+|.++++.+
T Consensus 184 ~L~~~~r~vl~l~~~~----g~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 184 SLPEREQLVLSLYYQE----EL----NLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred hCCHHHHHHHHhHhcc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3788888888776654 22 4578999999999999999999999997754
No 90
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=45.73 E-value=35 Score=29.21 Aligned_cols=49 Identities=14% Similarity=0.188 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++.-.+.+. .+ -.++|+.+|++..-|.++...++++++..+
T Consensus 119 ~Lp~~~r~v~~L~~~~g--~s------~~EIA~~lgis~~tV~~~l~ra~~~~~~~l 167 (172)
T PRK12523 119 KLSSKARAAFLYNRLDG--MG------HAEIAERLGVSVSRVRQYLAQGLRQCYIAL 167 (172)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 48999999888766652 23 368999999999999999999999986543
No 91
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=45.71 E-value=43 Score=28.39 Aligned_cols=49 Identities=16% Similarity=0.209 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++..-+++. + .-.++|+.+|+|+..|.++..-+|.++++.+
T Consensus 119 ~L~~~~r~i~~l~~~~g----~----s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l 167 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD----L----TIKEIAEVMNKPEGTVKTYLHRALKKLKKRL 167 (169)
T ss_pred hCCHHHhHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 48888888887766652 2 3468999999999999999999999987644
No 92
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=44.89 E-value=38 Score=29.77 Aligned_cols=50 Identities=18% Similarity=0.145 Sum_probs=40.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhH
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMV 178 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~ 178 (313)
.||+..+.++.-.+.+ .+ .-.++|+.+|++...|.++...+|.++++.+.
T Consensus 116 ~Lp~~~r~i~~L~~~~----g~----s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 116 QLPDDQREAIILVGAS----GF----AYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4899998888776665 23 23589999999999999999999999977653
No 93
>PRK04217 hypothetical protein; Provisional
Probab=44.61 E-value=54 Score=27.47 Aligned_cols=49 Identities=18% Similarity=0.232 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.++.+.+.++..++.+. + .-.++|+.+|++...|.+.+..++.+++..+
T Consensus 42 ~Lt~eereai~l~~~eG----l----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 42 FMTYEEFEALRLVDYEG----L----TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred cCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 48889998888887652 2 4567999999999999999999998886544
No 94
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=44.11 E-value=41 Score=30.25 Aligned_cols=49 Identities=24% Similarity=0.375 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++...|.+ .+ .-.++|+.+|++...|..|...++.++++.+
T Consensus 178 ~L~~~~r~vl~l~y~~----~~----s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l 226 (227)
T TIGR02980 178 ALPERERRILLLRFFE----DK----TQSEIAERLGISQMHVSRLLRRALKKLREQL 226 (227)
T ss_pred cCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 4899999888877664 22 4578999999999999999999999987643
No 95
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=43.59 E-value=50 Score=23.50 Aligned_cols=51 Identities=18% Similarity=0.191 Sum_probs=37.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHHH
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVEE 180 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~e 180 (313)
.|++....+|+-+..- + .-.++|...|++++.|.++..+.+.|+.-.-..+
T Consensus 3 ~LT~~E~~vl~~l~~G-----~----~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~~~~ 53 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG-----M----SNKEIAEELGISEKTVKSHRRRIMKKLGVKNRAE 53 (58)
T ss_dssp SS-HHHHHHHHHHHTT-----S-----HHHHHHHHTSHHHHHHHHHHHHHHHHT-SSHHH
T ss_pred ccCHHHHHHHHHHHhc-----C----CcchhHHhcCcchhhHHHHHHHHHHHhCCCCHHH
Confidence 4788888888665443 3 4578999999999999999999999986544333
No 96
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=43.12 E-value=34 Score=30.24 Aligned_cols=49 Identities=22% Similarity=0.192 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++.-.+.+ .+ .-.++|..+|++...|.+++.-+|.++++.+
T Consensus 113 ~Lp~~~r~v~~L~~~~----g~----s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 113 QLPDEQREALILVGAS----GF----SYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred hCCHHHhHHhhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4899999998877665 33 2467999999999999999999999997655
No 97
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=42.94 E-value=44 Score=28.74 Aligned_cols=49 Identities=22% Similarity=0.259 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++.-.+.+ .+ .-.++|+.+|++...|.++...+|.++++.+
T Consensus 135 ~L~~~~r~vl~l~~~~----~~----s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 135 ALSPEERRVIEVLYYQ----GY----THREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 4899998888766554 22 3478999999999999999999999987644
No 98
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=42.87 E-value=49 Score=29.64 Aligned_cols=49 Identities=18% Similarity=0.174 Sum_probs=38.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++...+.+. .+ -.++|+.+|++...|.++..-+|.++++.+
T Consensus 138 ~L~~~~r~v~~L~~~~g--~s------~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEG--LS------YEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 38888888776555542 23 368999999999999999999999997655
No 99
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=42.65 E-value=24 Score=30.80 Aligned_cols=49 Identities=20% Similarity=0.228 Sum_probs=37.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++.-.+.+ .+ .-.++|+.+|++...|.++...+|+++++.+
T Consensus 139 ~L~~~~r~i~~l~~~~----g~----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 139 TLPDEQREVFLLREHG----DL----ELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred hCCHhHhhheeeehcc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3777777777655443 22 3468999999999999999999999998765
No 100
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=42.05 E-value=54 Score=28.78 Aligned_cols=49 Identities=14% Similarity=0.124 Sum_probs=39.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+.++.++.-.+.+ .| .-.++|+.+|++...|.+++.-+|.++++-+
T Consensus 136 ~L~~~~r~i~~L~~~~----g~----s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 136 ALPERQRQAVVLRHIE----GL----SNPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4888888888766554 33 2478999999999999999999999997654
No 101
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=41.69 E-value=70 Score=28.01 Aligned_cols=51 Identities=14% Similarity=0.182 Sum_probs=41.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHH
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVE 179 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~ 179 (313)
.||+..+.++...|.+. - .-.++|+.+|++..-|.+...-+|+++++-+..
T Consensus 131 ~L~~~~r~v~~l~~~~g--~------s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~ 181 (188)
T TIGR02943 131 HLPEQTARVFMMREVLG--F------ESDEICQELEISTSNCHVLLYRARLSLRACLSI 181 (188)
T ss_pred hCCHHHHHHHHHHHHhC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 48888888887766652 2 347899999999999999999999999876643
No 102
>PF12998 ING: Inhibitor of growth proteins N-terminal histone-binding; InterPro: IPR024610 Histones undergo numerous post-translational modifications, including acetylation and methylation, at residues which are then probable docking sites for various chromatin remodelling complexes. Inhibitor of growth proteins (INGs) specifically bind to residues that have been thus modified. INGs carry a well-characterised C-terminal PHD-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3), as well as this N-terminal domain that binds unmodified H3 tails. Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail. This entry represents the N-terminal histone binding domain found in inhibitor proteins.; PDB: 4AFL_A.
Probab=41.68 E-value=1.3e+02 Score=23.59 Aligned_cols=69 Identities=12% Similarity=0.088 Sum_probs=45.8
Q ss_pred hccHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccc-cHHHHHHHHHhhcccchHHHHHHHH
Q 040555 8 VSSKLAWHELQLLALKVYWKYKLYCQQMQSVVASFETVAGLGHAAP-YISFAFKAISKHFCCLKNAILDQIH 78 (313)
Q Consensus 8 ~~~~~~~~~l~~~l~ev~~ry~~y~~qmq~v~~sfe~~ag~g~a~~-y~~lal~~~Sr~Fr~l~~~i~~ql~ 78 (313)
+..++ .+.+.++.|+|.++....+++...+..|-...+.+...+ =..-.+..|...+..+...--..+.
T Consensus 13 LP~el--~r~l~~irelD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~~~~l~deKv~ 82 (105)
T PF12998_consen 13 LPAEL--QRNLTLIRELDAKSQDLLEELDQQIQKFIKNHGSPSLSPEKRRELLKEIQEEYERALELSDEKVA 82 (105)
T ss_dssp HHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTS--S-HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ChHHH--HHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhcccccCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445 789999999999999999999999999988877643222 2333445555555555444333333
No 103
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=41.42 E-value=46 Score=29.95 Aligned_cols=48 Identities=23% Similarity=0.345 Sum_probs=39.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKP 176 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~ 176 (313)
.||+..+.++...|.+ .+ .-.++|+.+|++...|..+...++.++++.
T Consensus 175 ~L~~~~r~il~l~y~~----~~----s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 175 SLSEREQLVLSLYYYE----EL----NLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred hCCHHHHHHHHHHHhC----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4888888888887765 22 347899999999999999999999988754
No 104
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=41.41 E-value=70 Score=27.54 Aligned_cols=52 Identities=15% Similarity=0.103 Sum_probs=42.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHHH
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVEE 180 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~e 180 (313)
.||+..+.++.-.+.++ - .-.++|+.+|++...|.+....+|.++++-+..+
T Consensus 117 ~Lp~~~r~i~~l~~~e~--~------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~ 168 (179)
T PRK12543 117 KLPYKLRQVIILRYLHD--Y------SQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIE 168 (179)
T ss_pred hCCHHHHHHHHHHHHcc--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 48999988887766653 1 3468999999999999999999999998876544
No 105
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=41.39 E-value=40 Score=29.18 Aligned_cols=49 Identities=20% Similarity=0.259 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++...+.+ .+ .-.++|+.+|++...|.+....+|.++++-+
T Consensus 122 ~L~~~~r~i~~l~~~~----g~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 122 ELNESNRQVFKYKVFY----NL----TYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4899999988775554 22 3468999999999999999999999987655
No 106
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=41.34 E-value=24 Score=26.67 Aligned_cols=20 Identities=20% Similarity=0.501 Sum_probs=17.7
Q ss_pred HHHHHHHHhCCChHHHhhhh
Q 040555 147 DKQILAKQTGLSKNQVSNWF 166 (313)
Q Consensus 147 eK~~LA~~tgLs~~QV~NWF 166 (313)
.-.+||.++|++..+|..|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 45789999999999999994
No 107
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=40.75 E-value=47 Score=30.26 Aligned_cols=49 Identities=22% Similarity=0.171 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++.-.|.++ | .-.++|+.+|++...|.++...+|.++++.+
T Consensus 134 ~Lp~~~R~v~~L~y~eg----~----s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 134 KLPVEYREVLVLRELED----M----SYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred cCCHHHHhHhhhHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999998877763 2 2368999999999999999999999987765
No 108
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=40.55 E-value=58 Score=28.17 Aligned_cols=48 Identities=13% Similarity=0.128 Sum_probs=38.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKP 176 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~ 176 (313)
.||++.+.++..-|.+ .+ .-.++|+.+|++...|.+|...+|.++++-
T Consensus 133 ~L~~~~r~i~~l~~~~----~~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 133 QLEPARRNCILHAYVD----GC----SHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 4888888877666554 22 347899999999999999999999888653
No 109
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=40.51 E-value=92 Score=25.66 Aligned_cols=49 Identities=24% Similarity=0.201 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhH
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMV 178 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~ 178 (313)
.|++...++|+-+ .+ .|. ..++|+.++++.+.|.++..|.+++..-.-.
T Consensus 149 ~lt~~e~~vl~l~-~~----g~~----~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~~ 197 (211)
T PRK15369 149 LLTPRERQILKLI-TE----GYT----NRDIAEQLSISIKTVETHRLNMMRKLDVHKV 197 (211)
T ss_pred CCCHHHHHHHHHH-HC----CCC----HHHHHHHhCCCHHHHHHHHHHHHHHhCCCCH
Confidence 4899999998774 44 232 4789999999999999999999999854333
No 110
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=40.14 E-value=29 Score=23.76 Aligned_cols=21 Identities=24% Similarity=0.235 Sum_probs=19.1
Q ss_pred HHHHHhCCChHHHhhhhhhhH
Q 040555 150 ILAKQTGLSKNQVSNWFINAR 170 (313)
Q Consensus 150 ~LA~~tgLs~~QV~NWF~N~R 170 (313)
+||+.+|++...|+.|+.|.+
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999874
No 111
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=39.88 E-value=67 Score=28.44 Aligned_cols=50 Identities=20% Similarity=0.269 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhH
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMV 178 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~ 178 (313)
.||+..+.++.-.+++ .+ .-.++|..+|++...|.+....+|.++++-+.
T Consensus 139 ~Lp~~~r~v~~L~~~e----g~----s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 188 (201)
T PRK12545 139 HLPEQIGRVFMMREFL----DF----EIDDICTELTLTANHCSVLLYRARTRLRTCLS 188 (201)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4888888888776665 22 23689999999999999999999999987653
No 112
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=39.70 E-value=72 Score=26.51 Aligned_cols=43 Identities=16% Similarity=0.360 Sum_probs=33.7
Q ss_pred ChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhh
Q 040555 123 PDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINA 169 (313)
Q Consensus 123 p~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~ 169 (313)
....+..+.+|+.+|+..+ + .-.+||+.+|+++..+..+|+..
T Consensus 7 ~~~~i~~~~~~I~~~~~~~-~---sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 7 DAITIHSILDWIEDNLESP-L---SLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred cHHHHHHHHHHHHHhcCCC-C---CHHHHHHHHCcCHHHHHHHHHHH
Confidence 3445667788999977665 3 45789999999999999999865
No 113
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=39.45 E-value=65 Score=27.46 Aligned_cols=51 Identities=14% Similarity=0.171 Sum_probs=39.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHH
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVE 179 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~ 179 (313)
.||+....++.-.+.+. - .-.++|..+|++...|......+|.++++-+.+
T Consensus 119 ~L~~~~r~i~~l~~~~~--~------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~ 169 (173)
T PRK12522 119 LLNEKYKTVLVLYYYEQ--Y------SYKEMSEILNIPIGTVKYRLNYAKKQMREHLEG 169 (173)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 47888877776655542 2 236899999999999999999999999876543
No 114
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=39.35 E-value=46 Score=28.29 Aligned_cols=49 Identities=20% Similarity=0.226 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++.--+.+ .+ .-.++|+.+|++..-|.+...-+|.++++.+
T Consensus 118 ~L~~~~r~vl~L~~~~----g~----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 118 QLSPEHRAVLVRSYYR----GW----STAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 4899999988876665 23 2468999999999999999999999987755
No 115
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=38.86 E-value=30 Score=23.71 Aligned_cols=24 Identities=29% Similarity=0.524 Sum_probs=17.5
Q ss_pred HHHHHHHHhCCChHHHhhhhhhhH
Q 040555 147 DKQILAKQTGLSKNQVSNWFINAR 170 (313)
Q Consensus 147 eK~~LA~~tgLs~~QV~NWF~N~R 170 (313)
...++|+.+|++...|.+|....+
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT---
T ss_pred CHHHHHHHHCcCHHHHHHHHHHcc
Confidence 467899999999999999977654
No 116
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=38.28 E-value=71 Score=29.41 Aligned_cols=50 Identities=14% Similarity=0.122 Sum_probs=39.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhH
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMV 178 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~ 178 (313)
.||+.++.++.-.+.+ .+ .-.++|+.+|++...|.+....+|.++++.+.
T Consensus 171 ~Lp~~~R~v~~L~~~e----g~----s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 171 RLPEQQRIAVILSYHE----NM----SNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred hCCHHHHHHhhhHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3788888887665554 22 34789999999999999999999999987653
No 117
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=37.70 E-value=47 Score=28.96 Aligned_cols=47 Identities=15% Similarity=0.009 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhch
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWK 175 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk 175 (313)
.||+.++.++.-.+.+. + .-.++|+.+|++...|.++..-+|.++++
T Consensus 130 ~Lp~~~r~v~~L~~~~g----~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 130 DLTTDQREALLLTQLLG----L----SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred hCCHHHhHHhhhHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 48888888887766652 2 34689999999999999999999999876
No 118
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=37.60 E-value=70 Score=27.69 Aligned_cols=49 Identities=16% Similarity=0.144 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++.-.+.+. + .-.++|+.+|++...|.++...+|+++++-+
T Consensus 131 ~L~~~~r~v~~l~~~~g----~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 131 RLPEKMRLAIQAVKLEG----L----SVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred hCCHHHHHHHHHHHHcC----C----cHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 48999999998766652 2 3478999999999999999999999987654
No 119
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=36.89 E-value=71 Score=27.26 Aligned_cols=49 Identities=18% Similarity=0.190 Sum_probs=37.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+....++.-.+.+ .+ .-.++|+.+|++...|.+....+|.++++.+
T Consensus 136 ~L~~~~r~il~l~~~~----~~----s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T PRK09641 136 QLPEKYRTVIVLKYIE----DL----SLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHHHHhhhHHhh----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3777777777544332 22 3478999999999999999999999987644
No 120
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=36.72 E-value=30 Score=23.96 Aligned_cols=22 Identities=23% Similarity=0.324 Sum_probs=18.8
Q ss_pred HHHHHHHHhCCChHHHhhhhhh
Q 040555 147 DKQILAKQTGLSKNQVSNWFIN 168 (313)
Q Consensus 147 eK~~LA~~tgLs~~QV~NWF~N 168 (313)
...+||+.+|+++..|+.|..+
T Consensus 11 s~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 11 SQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTT
T ss_pred CHHHHHHHhCCCcchhHHHhcC
Confidence 3478999999999999999999
No 121
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=36.21 E-value=62 Score=28.29 Aligned_cols=47 Identities=17% Similarity=0.134 Sum_probs=36.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKP 176 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~ 176 (313)
.||+..+.++.. +.+ .| .-.++|..+|++...|.+.+..+|.++++-
T Consensus 155 ~L~~~~r~vl~l-~~e----~~----s~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 155 LLSELEKEVLEL-YLD----GK----SYQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred hCCHHHHHHHHH-HHc----cC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 478888888877 444 22 347899999999999999888888887664
No 122
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=36.11 E-value=63 Score=28.66 Aligned_cols=49 Identities=20% Similarity=0.149 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++..-+.+. + .-.++|+.+|++...|.++...+|.++++-+
T Consensus 133 ~Lp~~~r~v~~l~~~~g----~----s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l 181 (196)
T PRK12535 133 ALPPERREALILTQVLG----Y----TYEEAAKIADVRVGTIRSRVARARADLIAAT 181 (196)
T ss_pred cCCHHHHHHhhhHHHhC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 38888888887666652 1 3478999999999999999999999987655
No 123
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=35.87 E-value=84 Score=26.28 Aligned_cols=49 Identities=18% Similarity=0.209 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++.-.|++ .+ .-.++|+.+|++...|.....-+|.++++-+
T Consensus 109 ~L~~~~r~v~~l~~~~----~~----s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 109 ELPARTRYAFEMYRLH----GE----TQKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4888998888766654 22 2478999999999999999888888887654
No 124
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=35.75 E-value=84 Score=26.32 Aligned_cols=49 Identities=22% Similarity=0.245 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+....++.-.+.+. - .-.++|..+|++..-|.+....+|.++++.+
T Consensus 105 ~L~~~~r~v~~l~~~~~--~------s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l 153 (159)
T PRK12527 105 ELPPACRDSFLLRKLEG--L------SHQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153 (159)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 38999999988877653 2 2478999999999999999999998887654
No 125
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=35.51 E-value=1.1e+02 Score=25.40 Aligned_cols=46 Identities=15% Similarity=0.239 Sum_probs=30.9
Q ss_pred CCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhH
Q 040555 118 SQRALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINAR 170 (313)
Q Consensus 118 ~rr~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R 170 (313)
+++.++.+.....-....+ +.+ ....+|+..|++..+|.+|..-.+
T Consensus 9 ~rr~ys~EfK~~aV~~~~~---~g~----sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFE---PGM----TVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred CCCCCCHHHHHHHHHHHHc---CCC----CHHHHHHHHCcCHHHHHHHHHHHh
Confidence 3455777765444333344 343 456789999999999999966544
No 126
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=35.50 E-value=74 Score=27.56 Aligned_cols=48 Identities=17% Similarity=0.184 Sum_probs=36.8
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 122 LPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 122 lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
||+..+.++.-.+.+ .| .-.++|+.+|++...|.+....+|+++++.+
T Consensus 139 L~~~~r~v~~l~~~~----g~----s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 139 LPEDLRTALTLREFD----GL----SYEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred CCHHHhHHHhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 677776666554443 33 3468999999999999999999999997755
No 127
>PF14943 MRP-S26: Mitochondrial ribosome subunit S26
Probab=35.50 E-value=42 Score=30.23 Aligned_cols=24 Identities=21% Similarity=0.379 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 040555 22 LKVYWKYKLYCQQMQSVVASFETV 45 (313)
Q Consensus 22 ~ev~~ry~~y~~qmq~v~~sfe~~ 45 (313)
-|+.++|.+|..+|.+|-+.|-.-
T Consensus 27 ~el~~~~~~Yr~~m~alR~~f~ee 50 (170)
T PF14943_consen 27 KELKRRYNNYRTQMRALRSEFREE 50 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999888543
No 128
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=35.12 E-value=98 Score=26.50 Aligned_cols=49 Identities=22% Similarity=0.261 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++.-.+.+ .+ .-.++|+.+|++...|.++..-+|.++++-+
T Consensus 100 ~L~~~~r~v~~l~~~~----g~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 100 ELPDEYREAIRLTELE----GL----SQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4899999888876665 33 3478999999999999999999998887654
No 129
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=35.08 E-value=90 Score=28.52 Aligned_cols=56 Identities=14% Similarity=0.109 Sum_probs=42.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHHH
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVEE 180 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~e 180 (313)
.||+..+.+|...|.-+-..++ .-.++|..+|++...|+.+...++.+++..+..+
T Consensus 176 ~L~~~er~vl~l~ygl~~~~~~----t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~ 231 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDGRPH----TLEEVGKEFNVTRERIRQIESKALRKLRHPSRSK 231 (238)
T ss_pred hCCHHHHHHHHHHhCCCCCCCc----cHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHh
Confidence 4888888888777621000222 4678999999999999999999999998876443
No 130
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=35.04 E-value=85 Score=28.38 Aligned_cols=53 Identities=19% Similarity=0.119 Sum_probs=39.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++.-.|.-+....+ .-.++|+.+|++...|.++...+|.++++.+
T Consensus 178 ~Lp~~~R~v~~L~y~l~~~eg~----s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l 230 (234)
T PRK08301 178 KLSDREKQIMELRFGLNGGEEK----TQKEVADMLGISQSYISRLEKRIIKRLKKEI 230 (234)
T ss_pred hCCHHHHHHHHHHhccCCCCCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4888888888766521001122 3578999999999999999999999998754
No 131
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=35.00 E-value=78 Score=27.86 Aligned_cols=48 Identities=21% Similarity=0.316 Sum_probs=36.8
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 122 LPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 122 lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
+++....++.-.++. .| .-.++|+.+|+|+..|.+.+..+|.++.+.+
T Consensus 136 l~~~~~~~v~l~~~~----Gl----s~~EIA~~lgiS~~tV~r~l~~aR~~l~~~l 183 (185)
T PF07638_consen 136 LDPRQRRVVELRFFE----GL----SVEEIAERLGISERTVRRRLRRARAWLRREL 183 (185)
T ss_pred cCHHHHHHHHHHHHC----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 566666666665553 55 5678999999999999999999998876543
No 132
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=35.00 E-value=1.2e+02 Score=26.58 Aligned_cols=52 Identities=19% Similarity=0.182 Sum_probs=41.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhHHH
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMVEE 180 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~e 180 (313)
.||+..+.++...+.++ + .-.++|..+|++..-|.++..-+|.++++.+.+.
T Consensus 128 ~Lp~~~r~v~~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 179 (188)
T PRK12517 128 KLDPEYREPLLLQVIGG----F----SGEEIAEILDLNKNTVMTRLFRARNQLKEALEKP 179 (188)
T ss_pred hCCHHHHHHHHHHHHhC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 48999999888777663 2 2368999999999999999999999987766433
No 133
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=34.69 E-value=66 Score=27.82 Aligned_cols=30 Identities=17% Similarity=0.060 Sum_probs=25.8
Q ss_pred HHHHHHHHhCCChHHHhhhhhhhHhhhchh
Q 040555 147 DKQILAKQTGLSKNQVSNWFINARVRLWKP 176 (313)
Q Consensus 147 eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~ 176 (313)
.-.++|+.+|++...|.+++.-+|+++++-
T Consensus 167 s~~eIA~~l~~s~~tV~~~l~r~r~~L~~~ 196 (198)
T TIGR02859 167 SYQEIACDLNRHVKSIDNALQRVKRKLEKY 196 (198)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 457899999999999999999998888653
No 134
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=34.66 E-value=89 Score=27.24 Aligned_cols=49 Identities=24% Similarity=0.314 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++.-.+.+ .+ .-.++|..+|++...|.+.+..+|.++++-+
T Consensus 106 ~L~~~~r~i~~l~~~~----g~----~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 106 ALPEKYAEALRLTELE----GL----SQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred hCCHHHHHHHHHHHhc----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4888888888766554 33 3478999999999999999999999987654
No 135
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=34.55 E-value=78 Score=27.35 Aligned_cols=47 Identities=11% Similarity=0.099 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhch
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWK 175 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk 175 (313)
.||+.++.++.-.+.+. . .-.++|+.+|++..-|.+.+..++++...
T Consensus 127 ~Lp~~~R~v~~L~~~~g--~------s~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG--M------KQKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 49999999888776652 2 34789999999999999999998888754
No 136
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=34.30 E-value=86 Score=28.89 Aligned_cols=48 Identities=19% Similarity=0.198 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKP 176 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~ 176 (313)
.||+..+.++...|.+ .+ .-.++|..+|+|...|.+++..+|.++++-
T Consensus 201 ~L~~~~r~vl~l~~~~----~~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 201 QLSEKEQLVISLFYKE----EL----TLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred cCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3788888888776664 22 357899999999999999999999998753
No 137
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=34.05 E-value=63 Score=28.25 Aligned_cols=50 Identities=16% Similarity=0.107 Sum_probs=40.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhH
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMV 178 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~ 178 (313)
.||+..+.++.-.+.+. + .-.++|+.+|++...|.....-+|.++++.+.
T Consensus 111 ~Lp~~~R~v~~L~~~~g----~----s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 111 KLPQDQREALILVGASG----F----SYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred hCCHHHHHHhhHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 48999988887766652 2 34689999999999999999999999877653
No 138
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=33.93 E-value=71 Score=29.72 Aligned_cols=50 Identities=20% Similarity=0.169 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhH
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMV 178 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~ 178 (313)
.||+..+.++...|.+ .+ .-.++|..+|++...|+.+..-++.++++.+.
T Consensus 203 ~L~~~~r~vl~l~y~~----~~----s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~ 252 (256)
T PRK07408 203 QLEERTREVLEFVFLH----DL----TQKEAAERLGISPVTVSRRVKKGLDQLKKLLQ 252 (256)
T ss_pred cCCHHHHHHHHHHHHC----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 3788888888777664 22 45789999999999999999999999877653
No 139
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=33.83 E-value=69 Score=27.66 Aligned_cols=49 Identities=27% Similarity=0.354 Sum_probs=39.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+.++.++...+.+. + .-.++|+.+|++...|.++..-+|.++++-+
T Consensus 127 ~L~~~~r~v~~l~~~~g----~----s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 127 SLPIKYREVIYLFYYEE----L----SIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred hCCHHHhhHhHhHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999988887766552 2 2368999999999999999999999987644
No 140
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=33.67 E-value=33 Score=23.48 Aligned_cols=23 Identities=13% Similarity=0.042 Sum_probs=20.3
Q ss_pred HHHHHHHhCCChHHHhhhhhhhH
Q 040555 148 KQILAKQTGLSKNQVSNWFINAR 170 (313)
Q Consensus 148 K~~LA~~tgLs~~QV~NWF~N~R 170 (313)
-.+||+.+|++...|+.|..+++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 47899999999999999997764
No 141
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=33.41 E-value=45 Score=28.35 Aligned_cols=48 Identities=23% Similarity=0.166 Sum_probs=37.4
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 122 LPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 122 lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
||+..+.+|...+.+ .+ .-.++|+.+|++...|.+.+..+|.++++.+
T Consensus 121 L~~~~r~vl~l~~~~----g~----s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 121 LSLEHRAVLVLHDLE----DL----PQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred CCHHHeeeeeehHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 677777766655443 22 3578999999999999999999999997754
No 142
>cd07597 BAR_SNX8 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 8. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX8 and the yeast counterpart Mvp1p are involved in sorting and delivery of late-Golgi proteins, such as carboxypeptidase Y, to vacuoles. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=33.26 E-value=1.9e+02 Score=27.06 Aligned_cols=70 Identities=17% Similarity=0.202 Sum_probs=54.0
Q ss_pred cHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcc----------ccHHHHHHHHHhhcccchHHHHHHHHH
Q 040555 10 SKLAWHELQLLALKVYWKYKLYCQQMQSVVASFETVAGLGHAA----------PYISFAFKAISKHFCCLKNAILDQIHV 79 (313)
Q Consensus 10 ~~~~~~~l~~~l~ev~~ry~~y~~qmq~v~~sfe~~ag~g~a~----------~y~~lal~~~Sr~Fr~l~~~i~~ql~~ 79 (313)
+...|.||-.+++.+.+|=++.-..+..+...+..++-..... +--.-++..|+.||..+-+...+|-..
T Consensus 34 l~~~~~~l~~l~er~~kR~~~~A~d~~~f~~~l~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~s~~~~~~s~~~~~~a~~ 113 (246)
T cd07597 34 LLESWTKLRVLAERYEKRSQQQAADRAEFARLLNSLGELTARLYPWAGDSDTWGDINEGLSSLSKHFQLLSDLSEDEARA 113 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4578999999999999999999999999998888887655432 223467788999998887766555544
No 143
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=33.11 E-value=84 Score=28.46 Aligned_cols=52 Identities=29% Similarity=0.423 Sum_probs=41.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRL 173 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~ 173 (313)
.|++.++++|+..|..=+. -||-...-.+||+++|+++.-+..=..++=+|+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYF-d~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl 206 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYF-DYPRRVSLKDLAKELGISKSTLSEHLRRAERKL 206 (215)
T ss_pred cCCHHHHHHHHHHHHcCCC-CCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 5999999999988775333 358999999999999999999877555544444
No 144
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=32.76 E-value=74 Score=27.86 Aligned_cols=49 Identities=22% Similarity=0.133 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+.++.++.-.+.+ .+ .-.++|+.+|++..-|.++..-+|.++++-+
T Consensus 111 ~Lp~~~R~v~~L~~~e----g~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~ 159 (182)
T PRK12511 111 DLPEEQRAALHLVAIE----GL----SYQEAAAVLGIPIGTLMSRIGRARAALRAFE 159 (182)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 4899999999887665 33 2468999999999999999999999887644
No 145
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=32.34 E-value=99 Score=28.84 Aligned_cols=49 Identities=22% Similarity=0.425 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++...|.+. + .-.++|..+|++...|......++.++++.+
T Consensus 212 ~L~~~~r~vl~l~~~~~----~----s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 260 (268)
T PRK06288 212 TLPEREKKVLILYYYED----L----TLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260 (268)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 48888888888777652 2 3578999999999999999999999997765
No 146
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=32.29 E-value=97 Score=25.97 Aligned_cols=46 Identities=17% Similarity=0.224 Sum_probs=37.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhc
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLW 174 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~k 174 (313)
.||+.++.++.-.+.+. + .-.++|+.+|++...|.++...+++++.
T Consensus 113 ~L~~~~r~v~~L~~~~g----~----s~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 113 GLPPLVKRAFLLAQVDG----L----GYGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred HCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 48999999887776652 2 2368999999999999999999988764
No 147
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=32.26 E-value=92 Score=20.93 Aligned_cols=45 Identities=22% Similarity=0.199 Sum_probs=31.3
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhch
Q 040555 122 LPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWK 175 (313)
Q Consensus 122 lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk 175 (313)
|++....++..+ .. .+ ...++|+.++++...|..|....+.+...
T Consensus 1 l~~~e~~i~~~~-~~----~~----s~~eia~~l~~s~~tv~~~~~~~~~~l~~ 45 (57)
T cd06170 1 LTPREREVLRLL-AE----GK----TNKEIADILGISEKTVKTHLRNIMRKLGV 45 (57)
T ss_pred CCHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 355566666443 22 22 55789999999999999999877666543
No 148
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=31.12 E-value=1e+02 Score=26.60 Aligned_cols=48 Identities=19% Similarity=0.243 Sum_probs=38.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKP 176 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~ 176 (313)
.||+....++...|.+ .+ .-.++|..+|++...|.+-...+|.++++-
T Consensus 137 ~L~~~~r~i~~l~~~~----g~----s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 184 (187)
T PRK12534 137 ELEPPRSELIRTAFFE----GI----TYEELAARTDTPIGTVKSWIRRGLAKLKAC 184 (187)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence 3888888888777664 22 346899999999999999999999888754
No 149
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=30.57 E-value=46 Score=21.32 Aligned_cols=23 Identities=26% Similarity=0.354 Sum_probs=20.3
Q ss_pred HHHHHHHhCCChHHHhhhhhhhH
Q 040555 148 KQILAKQTGLSKNQVSNWFINAR 170 (313)
Q Consensus 148 K~~LA~~tgLs~~QV~NWF~N~R 170 (313)
...+|+.+|++...|.+|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 45899999999999999998864
No 150
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=30.41 E-value=77 Score=29.79 Aligned_cols=48 Identities=27% Similarity=0.434 Sum_probs=38.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKP 176 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~ 176 (313)
.||+..+.+|...|.+ .+ .-.++|..+|++...|..+...++.++++.
T Consensus 215 ~L~~rer~vl~l~y~~----~~----t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 262 (264)
T PRK07122 215 ALPERERTVLVLRFFE----SM----TQTQIAERVGISQMHVSRLLAKTLARLRDQ 262 (264)
T ss_pred cCCHHHHHHHHHHhcC----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3778888888777654 33 347899999999999999999999988754
No 151
>cd00131 PAX Paired Box domain
Probab=29.92 E-value=1.9e+02 Score=24.40 Aligned_cols=46 Identities=15% Similarity=0.110 Sum_probs=32.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCC-------ChHHHhhhhhhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGL-------SKNQVSNWFINA 169 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgL-------s~~QV~NWF~N~ 169 (313)
.........+..+..+ ||..+-.|-.++-...|+ +...|+.||.++
T Consensus 75 ~~~~~~~~~i~~~v~~---~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 75 VATPEVVKKIEIYKQE---NPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred cCCHHHHHHHHHHHHH---CCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 3455556666677777 898888777666335566 999999998764
No 152
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=29.74 E-value=76 Score=29.72 Aligned_cols=50 Identities=18% Similarity=0.155 Sum_probs=38.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKP 176 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~ 176 (313)
.||+..+.+|...|.. ..+ -.-.++|+.+|+|...|+....++..|+++.
T Consensus 218 ~L~~rer~vl~l~y~~--~~~----~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~ 267 (270)
T TIGR02392 218 SLDARSRRIIEARWLD--DDK----LTLQELAAEYGVSAERIRQIEKNAMKKLKAA 267 (270)
T ss_pred cCCHHHHHHHHHHhcC--CCC----cCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3888888888776642 012 2357999999999999999999999998764
No 153
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=29.49 E-value=1.1e+02 Score=25.53 Aligned_cols=47 Identities=15% Similarity=0.078 Sum_probs=37.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhch
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWK 175 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk 175 (313)
.||+..+.++.-.|.+ .+ .-.++|+.+|++...|.+...-+|.++++
T Consensus 122 ~L~~~~r~vl~l~~~~----g~----s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQ----NL----PIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred hCCHHHHHHHHHHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3888888888776554 22 34789999999999999988888888765
No 154
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=29.27 E-value=1e+02 Score=27.80 Aligned_cols=48 Identities=15% Similarity=0.177 Sum_probs=37.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKP 176 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~ 176 (313)
.||+....++...|.+ . ..-.++|+.+|+|...|..+-..+..|+++.
T Consensus 183 ~L~~~e~~i~~~~~~~----~----~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~ 230 (231)
T TIGR02885 183 KLDERERQIIMLRYFK----D----KTQTEVANMLGISQVQVSRLEKKVLKKMKEK 230 (231)
T ss_pred cCCHHHHHHHHHHHHc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence 4788888888766654 2 2578899999999999999998888887653
No 155
>COG0133 TrpB Tryptophan synthase beta chain [Amino acid transport and metabolism]
Probab=28.61 E-value=4.5e+02 Score=26.68 Aligned_cols=52 Identities=10% Similarity=0.023 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccccHHHHHHHHHhhcc
Q 040555 15 HELQLLALKVYWKYKLYCQQMQSVVASFETVAGLGHAAPYISFAFKAISKHFC 67 (313)
Q Consensus 15 ~~l~~~l~ev~~ry~~y~~qmq~v~~sfe~~ag~g~a~~y~~lal~~~Sr~Fr 67 (313)
+-|+..|+|+++-|+.|..+=. ....|+.....=+.+|..-...+.+++|..
T Consensus 19 E~Lmpal~eLe~ay~~~~~D~~-F~~el~~~l~~Y~GRptpLy~a~~Lt~~~g 70 (396)
T COG0133 19 ETLMPALEELEKAYEKAKNDPE-FQAELDYLLKDYAGRPTPLYFAERLTEHLG 70 (396)
T ss_pred HHHHHHHHHHHHHHHHHhcCHH-HHHHHHHHHHHhCCCCChhHHHHHHHHhhC
Confidence 4689999999999999876632 444444443322222322233455666654
No 156
>PRK10072 putative transcriptional regulator; Provisional
Probab=28.22 E-value=42 Score=27.37 Aligned_cols=24 Identities=21% Similarity=0.252 Sum_probs=21.3
Q ss_pred HHHHHHHHhCCChHHHhhhhhhhH
Q 040555 147 DKQILAKQTGLSKNQVSNWFINAR 170 (313)
Q Consensus 147 eK~~LA~~tgLs~~QV~NWF~N~R 170 (313)
....||+.+|++...|++|...+|
T Consensus 48 TQ~elA~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 48 KIDDFARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCC
Confidence 367899999999999999998775
No 157
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=27.80 E-value=1.2e+02 Score=29.45 Aligned_cols=53 Identities=21% Similarity=0.199 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.+|...|.-+.... -.-.++|..+|++...|..+...++.++++.+
T Consensus 262 ~L~~~~R~vl~lrygL~~~e~----~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGYEA----ATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhccCCCCC----cCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 477788777765542111123 35678999999999999999999999998765
No 158
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=27.73 E-value=76 Score=27.62 Aligned_cols=50 Identities=20% Similarity=0.201 Sum_probs=38.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhH
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMV 178 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~ 178 (313)
.||+..+.++.-.+.+ .+ .-.++|+.+|++...|.++..-+|.++++.+.
T Consensus 131 ~Lp~~~r~i~~L~~~~----g~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 131 GLPEEFRQAVYLADVE----GF----AYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred hCCHHHhhheeehhhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3777777766554443 22 34789999999999999999999999987664
No 159
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=27.23 E-value=1.1e+02 Score=26.25 Aligned_cols=48 Identities=13% Similarity=0.076 Sum_probs=36.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKP 176 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~ 176 (313)
.||+..+.++.-.+.+. - .-.++|+.+|++...|.++...++.+..+-
T Consensus 119 ~L~~~~r~i~~l~~~~g--~------s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~ 166 (172)
T PRK09651 119 GLNGKTREAFLLSQLDG--L------TYSEIAHKLGVSVSSVKKYVAKATEHCLLF 166 (172)
T ss_pred hCCHHHhHHhhhhhccC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 38888888876655542 2 347899999999999999998888877543
No 160
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=27.20 E-value=46 Score=28.97 Aligned_cols=48 Identities=10% Similarity=0.043 Sum_probs=35.1
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 122 LPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 122 lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
||+..+.++.-.+.+ .+ .-.++|..+|++...|.++...+|.++++.+
T Consensus 135 L~~~~r~v~~l~~~~----g~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 182 (188)
T PRK09640 135 VNPIDREILVLRFVA----EL----EFQEIADIMHMGLSATKMRYKRALDKLREKF 182 (188)
T ss_pred cChhheeeeeeHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 566665555433333 22 3478999999999999999999999987654
No 161
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=26.82 E-value=57 Score=20.68 Aligned_cols=23 Identities=26% Similarity=0.335 Sum_probs=19.8
Q ss_pred HHHHHHHhCCChHHHhhhhhhhH
Q 040555 148 KQILAKQTGLSKNQVSNWFINAR 170 (313)
Q Consensus 148 K~~LA~~tgLs~~QV~NWF~N~R 170 (313)
...+|+.+|++...|..|..+.+
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~~ 35 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGKR 35 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 56899999999999999987653
No 162
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=26.48 E-value=1.2e+02 Score=25.88 Aligned_cols=47 Identities=15% Similarity=0.193 Sum_probs=37.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhch
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWK 175 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk 175 (313)
.||+..+.++.-.+.+ .+ .-.++|+.+|++...|.++..+++...+.
T Consensus 118 ~L~~~~r~v~~L~~~e----g~----s~~EIA~~l~is~~tV~~~l~ra~~~~~~ 164 (168)
T PRK12525 118 GLSGKARAAFLMSQLE----GL----TYVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4899999888776665 22 23689999999999999999888887654
No 163
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=26.35 E-value=94 Score=29.34 Aligned_cols=49 Identities=24% Similarity=0.070 Sum_probs=38.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+.++.++.-.+.+. -+ -.++|+.+|++...|.+.+.-+|.++++.+
T Consensus 142 ~Lp~~~R~v~~L~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 190 (324)
T TIGR02960 142 YLPPRQRAVLLLRDVLG--WR------AAETAELLGTSTASVNSALQRARATLDEVG 190 (324)
T ss_pred hCCHHHhhHhhhHHHhC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence 48888888876655542 22 368999999999999999999999987654
No 164
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=25.89 E-value=73 Score=26.27 Aligned_cols=46 Identities=26% Similarity=0.275 Sum_probs=33.4
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhch
Q 040555 122 LPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWK 175 (313)
Q Consensus 122 lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk 175 (313)
||+....++...+.+ .-.-.++|+.+|+++..|.++..-+|.++++
T Consensus 106 L~~~~r~i~~l~~~~--------g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 106 LPENYRTVLILREFK--------EFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred CCHhheeeeeehhhc--------cCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 555555555433222 2345789999999999999999999988865
No 165
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=25.59 E-value=1.2e+02 Score=27.42 Aligned_cols=52 Identities=21% Similarity=0.145 Sum_probs=38.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKP 176 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~ 176 (313)
.||+..+.++.-.|...-...+ .-.++|+.+|+++..|..+...+++++++.
T Consensus 174 ~L~~~~r~il~l~y~~~~~e~~----S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~ 225 (227)
T TIGR02846 174 VLDGREREVIEMRYGLGDGRRK----TQREIAKILGISRSYVSRIEKRALMKLYKE 225 (227)
T ss_pred hCCHHHHHHHHHHHcCCCCCCc----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4899999988877641000122 347899999999999999988888888764
No 166
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=25.05 E-value=1.4e+02 Score=22.49 Aligned_cols=41 Identities=24% Similarity=0.466 Sum_probs=26.4
Q ss_pred CCChhHHHHH---HHHHHHccCCCCCCHHHHHHHHHHhCCC-hHHHhhhh
Q 040555 121 ALPDHAVAVL---KTWLYENFLHPYPTDSDKQILAKQTGLS-KNQVSNWF 166 (313)
Q Consensus 121 ~lp~~a~~iL---~~wf~~h~~~PYPs~~eK~~LA~~tgLs-~~QV~NWF 166 (313)
.|++.+.++| .++..+ +.||. .-.+||+.+|+. ..-|..-.
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~---~G~~P--t~rEIa~~~g~~S~~tv~~~L 47 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIEE---NGYPP--TVREIAEALGLKSTSTVQRHL 47 (65)
T ss_dssp ---HHHHHHHHHHHHHHHH---HSS-----HHHHHHHHTSSSHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHH---cCCCC--CHHHHHHHhCCCChHHHHHHH
Confidence 3677777776 556666 78886 778899999997 77776533
No 167
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=24.64 E-value=61 Score=23.44 Aligned_cols=19 Identities=21% Similarity=0.216 Sum_probs=16.7
Q ss_pred HHHHHHhCCChHHHhhhhh
Q 040555 149 QILAKQTGLSKNQVSNWFI 167 (313)
Q Consensus 149 ~~LA~~tgLs~~QV~NWF~ 167 (313)
.++|+.+|++...|..|-.
T Consensus 4 ~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999943
No 168
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=24.58 E-value=1.4e+02 Score=27.64 Aligned_cols=49 Identities=22% Similarity=0.252 Sum_probs=38.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.|++..+.++...|.+ .+ .-.++|+.+|++...|+..-.++..++++.+
T Consensus 209 ~L~~~er~vi~~~~~~----~~----t~~eIA~~lgis~~~V~~~~~~al~kLr~~l 257 (258)
T PRK08215 209 KLNDREKLILNLRFFQ----GK----TQMEVAEEIGISQAQVSRLEKAALKHMRKYI 257 (258)
T ss_pred cCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 4888888888777654 22 3578999999999999999999988887643
No 169
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=24.43 E-value=74 Score=21.26 Aligned_cols=19 Identities=32% Similarity=0.277 Sum_probs=16.7
Q ss_pred HHHHHHhCCChHHHhhhhh
Q 040555 149 QILAKQTGLSKNQVSNWFI 167 (313)
Q Consensus 149 ~~LA~~tgLs~~QV~NWF~ 167 (313)
.++|+.+|++...|..|..
T Consensus 4 ~e~a~~~gv~~~tlr~~~~ 22 (49)
T cd04761 4 GELAKLTGVSPSTLRYYER 22 (49)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999954
No 170
>PHA01976 helix-turn-helix protein
Probab=24.41 E-value=60 Score=23.40 Aligned_cols=23 Identities=13% Similarity=0.342 Sum_probs=19.9
Q ss_pred HHHHHHHhCCChHHHhhhhhhhH
Q 040555 148 KQILAKQTGLSKNQVSNWFINAR 170 (313)
Q Consensus 148 K~~LA~~tgLs~~QV~NWF~N~R 170 (313)
..+||+.+|++...|++|....+
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46799999999999999987654
No 171
>smart00319 TarH Homologues of the ligand binding domain of Tar. Homologues of the ligand binding domain of the wild-type bacterial aspartate receptor, Tar.
Probab=24.25 E-value=2.6e+02 Score=22.18 Aligned_cols=67 Identities=12% Similarity=0.219 Sum_probs=40.3
Q ss_pred hhccHHhHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccccHHHHHHHHHhhcccchHHHHHH
Q 040555 7 YVSSKLAWHELQ----------LLALKVYWKYKLYCQQMQSVVASFETVAGLGHAAPYISFAFKAISKHFCCLKNAILDQ 76 (313)
Q Consensus 7 ~~~~~~~~~~l~----------~~l~ev~~ry~~y~~qmq~v~~sfe~~ag~g~a~~y~~lal~~~Sr~Fr~l~~~i~~q 76 (313)
...++..|.+.. .+.++|..+|+.|++-+..++..++. +....|.....+.+..-|..-...+..+
T Consensus 51 l~~a~~~~~~f~~~p~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~----~~~~~~~~~~~~~~~~~~~~~~~~w~~~ 126 (135)
T smart00319 51 LKQAEKNYKSYENMTALPRADRALDAELKEKFQQYITALQELIQILGN----GNLGAFFDQPTQGMQDGFDPAYRDWLQQ 126 (135)
T ss_pred HHHHHHHHHHHHcCcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHhc----CCcchHHhCchhhchhhhcHHHHHHHHH
Confidence 445667777664 55678999999998877766554332 2333454444444555566555554444
Q ss_pred H
Q 040555 77 I 77 (313)
Q Consensus 77 l 77 (313)
.
T Consensus 127 a 127 (135)
T smart00319 127 A 127 (135)
T ss_pred H
Confidence 3
No 172
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=23.73 E-value=1.5e+02 Score=26.97 Aligned_cols=54 Identities=20% Similarity=0.174 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhH
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMV 178 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~ 178 (313)
.||+..+.++...+.-+-... ..-.++|..+|++...|.++-..+++++++.+.
T Consensus 175 ~Lp~~~R~i~~l~y~~~~~e~----~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~ 228 (233)
T PRK05803 175 ILDEREKEVIEMRYGLGNGKE----KTQREIAKALGISRSYVSRIEKRALKKLFKELY 228 (233)
T ss_pred hCCHHHHHHHHHHhCCCCCCC----cCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 488888888877552100011 235789999999999999998888888877654
No 173
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=23.59 E-value=1.2e+02 Score=27.55 Aligned_cols=53 Identities=17% Similarity=0.068 Sum_probs=38.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++...+...-...+ .-.++|+.+|+++..|.++..-+|.++++.+
T Consensus 178 ~Lp~~~R~ii~L~~~l~~~eg~----s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l 230 (234)
T TIGR02835 178 KLNDREKKIMELRFGLVGGTEK----TQKEVADMLGISQSYISRLEKRILKRLKKEI 230 (234)
T ss_pred hCCHHHHHHHHHHHccCCCCCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 4888888888766530000122 3467999999999999999999999987643
No 174
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=23.37 E-value=1.1e+02 Score=21.71 Aligned_cols=30 Identities=20% Similarity=0.221 Sum_probs=20.3
Q ss_pred HHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 147 DKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 147 eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
....+|+.+|++..+|+.|-.+.+ ......
T Consensus 14 t~~~~a~~~~i~~~~i~~~e~g~~-~~~~~~ 43 (64)
T PF12844_consen 14 TQKDLAEKLGISRSTISKIENGKR-KPSVST 43 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS---BHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCc-CCCHHH
Confidence 456788899999999999988866 444333
No 175
>PF04740 LXG: LXG domain of WXG superfamily; InterPro: IPR006829 This group of putative transposases is found in Gram-positive bacteria, mostly Bacillus members and is thought to be a Cytosolic protein. However, we have also found a Bacillus subtilis bacteriophage SPbetac2 homologue (O64023 from SWISSPROT), possibly arising as a result of horizontal transfer. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=23.29 E-value=4.5e+02 Score=23.10 Aligned_cols=56 Identities=16% Similarity=0.122 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccccHHHHHHHHHhhcccchHH
Q 040555 15 HELQLLALKVYWKYKLYCQQMQSVVASFETVAGLGHAAPYISFAFKAISKHFCCLKNA 72 (313)
Q Consensus 15 ~~l~~~l~ev~~ry~~y~~qmq~v~~sfe~~ag~g~a~~y~~lal~~~Sr~Fr~l~~~ 72 (313)
..|....+.+..-++.+.+++..+..+++.++..+.. +.--|..++-.+|....-.
T Consensus 6 ~el~~~~~~~~~~~~~~~~~l~~l~~ai~~~~~~~~~--LkGka~dsiK~y~~~vh~p 61 (204)
T PF04740_consen 6 SELHSQAESTNSSLKELKEQLESLQKAINQFISSESS--LKGKAYDSIKNYFSEVHIP 61 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcch--hhhHHHHHHHHHHHHHHHH
Confidence 5788899999999999999999999999999877762 2223444444444443333
No 176
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=23.28 E-value=63 Score=23.90 Aligned_cols=23 Identities=30% Similarity=0.367 Sum_probs=20.2
Q ss_pred HHHHHHHhCCChHHHhhhhhhhH
Q 040555 148 KQILAKQTGLSKNQVSNWFINAR 170 (313)
Q Consensus 148 K~~LA~~tgLs~~QV~NWF~N~R 170 (313)
..+||+.+|++...|+.|..+.+
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46899999999999999997664
No 177
>PRK05572 sporulation sigma factor SigF; Validated
Probab=23.06 E-value=1.5e+02 Score=27.22 Aligned_cols=49 Identities=16% Similarity=0.197 Sum_probs=39.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+....++...|.+ . ..-.++|+.+|++...|..+-..+..++++.+
T Consensus 202 ~L~~~~~~v~~l~~~~----~----~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l 250 (252)
T PRK05572 202 ELDERERLIVYLRYFK----D----KTQSEVAKRLGISQVQVSRLEKKILKQMKEKL 250 (252)
T ss_pred cCCHHHHHHHHHHHhC----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3888888888776654 1 24578999999999999999999999887644
No 178
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=22.67 E-value=98 Score=21.24 Aligned_cols=40 Identities=20% Similarity=0.196 Sum_probs=21.5
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhh
Q 040555 120 RALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFI 167 (313)
Q Consensus 120 r~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~ 167 (313)
+.|+.+.+..+..++.+ . .-..++|+.+|.+.+-|.+|..
T Consensus 3 ~~Lt~~eR~~I~~l~~~----G----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQ----G----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS-----------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHc----C----CCHHHHHHHHCcCcHHHHHHHh
Confidence 34777888888888654 2 2456799999999999999875
No 179
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=22.49 E-value=2e+02 Score=25.09 Aligned_cols=49 Identities=22% Similarity=0.232 Sum_probs=36.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.+|.-.+.+ .+ .-.++|..+|++...|.+=.-.+|.++++.+
T Consensus 134 ~Lp~~~r~i~~l~~~~----g~----s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l 182 (192)
T PRK09643 134 RLPVEQRAALVAVDMQ----GY----SVADAARMLGVAEGTVKSRCARGRARLAELL 182 (192)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3888888888665554 22 3467999999999999888777787776544
No 180
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=22.31 E-value=90 Score=26.49 Aligned_cols=48 Identities=19% Similarity=0.111 Sum_probs=35.8
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 122 LPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 122 lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
||+..+.++.--+++ .+ .-.++|+.+|++...|.++...+|.++++.+
T Consensus 127 L~~~~r~v~~l~~~~----g~----s~~eIA~~l~is~~~V~~~l~ra~~~l~~~l 174 (176)
T PRK09638 127 LDPEFRAPVILKHYY----GY----TYEEIAKMLNIPEGTVKSRVHHGIKQLRKEW 174 (176)
T ss_pred CCHHHhheeeehhhc----CC----CHHHHHHHHCCChhHHHHHHHHHHHHHHHHh
Confidence 777777766443332 22 3478999999999999999999999987643
No 181
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=21.80 E-value=2.2e+02 Score=26.86 Aligned_cols=54 Identities=19% Similarity=0.207 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhhH
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPMV 178 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~ 178 (313)
.||+..+.+|.-.|.-+.... -.-.++|..+|++...|+.+...++.++++.+-
T Consensus 222 ~Lp~~~R~Vl~l~ygL~~~e~----~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~ 275 (285)
T TIGR02394 222 ELNERQREVLARRFGLLGYEP----ATLEEVAAEVGLTRERVRQIQVEALKKLRRILE 275 (285)
T ss_pred cCCHHHHHHHHHHhCCCCCCC----ccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 488888888876651000012 246789999999999999999999999988664
No 182
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=21.49 E-value=1.8e+02 Score=27.07 Aligned_cols=49 Identities=24% Similarity=0.346 Sum_probs=38.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchhh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKPM 177 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~ 177 (313)
.||+..+.++...|.+ .+ .-.++|..+|++...|+.+..-++.++++.+
T Consensus 205 ~L~~~er~vi~l~y~e----~~----t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 253 (257)
T PRK05911 205 ALEEKERKVMALYYYE----EL----VLKEIGKILGVSESRVSQIHSKALLKLRATL 253 (257)
T ss_pred cCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3777777777776654 22 3578999999999999999999999987654
No 183
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=21.49 E-value=1.7e+02 Score=27.51 Aligned_cols=48 Identities=17% Similarity=0.023 Sum_probs=37.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKP 176 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~ 176 (313)
.||+.++.++.-.+.+. .+ -.++|+.+|++..-|.+.+..+|+++++.
T Consensus 115 ~L~~~~R~v~~L~~~~g--~s------~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~ 162 (293)
T PRK09636 115 RLSPLERAAFLLHDVFG--VP------FDEIASTLGRSPAACRQLASRARKHVRAA 162 (293)
T ss_pred hCCHHHHHHHHHHHHhC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 38888888776554431 33 36899999999999999999999998764
No 184
>PHA00542 putative Cro-like protein
Probab=21.31 E-value=1.1e+02 Score=23.82 Aligned_cols=34 Identities=15% Similarity=0.219 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCChHHHhhhhhhhHhhhchhhHHH
Q 040555 147 DKQILAKQTGLSKNQVSNWFINARVRLWKPMVEE 180 (313)
Q Consensus 147 eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~~~~e 180 (313)
...+||+.+|++...|+.|............+++
T Consensus 33 Tq~elA~~lgIs~~tIsr~e~g~~~~p~~~~l~k 66 (82)
T PHA00542 33 SQEQIADATDVSQPTICRIYSGRHKDPRYSVVEK 66 (82)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHH
Confidence 4567999999999999999988754444444433
No 185
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=20.77 E-value=1.2e+02 Score=28.98 Aligned_cols=47 Identities=23% Similarity=0.137 Sum_probs=37.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhch
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWK 175 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk 175 (313)
.||+..+.++.-.+.+. + .-.++|+.+|++...|.+....+|.++++
T Consensus 153 ~Lp~~~R~v~~L~~~~g----~----s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 153 HLPPRQRAVLILRDVLG----W----SAAEVAELLDTSVAAVNSALQRARATLAE 199 (339)
T ss_pred hCCHHHhhhhhhHHhhC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence 47888888776665552 2 34689999999999999999999999876
No 186
>PF14644 DUF4456: Domain of unknown function (DUF4456)
Probab=20.60 E-value=2.2e+02 Score=26.01 Aligned_cols=56 Identities=14% Similarity=0.024 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccccHHHHHHHHHhhcccch
Q 040555 15 HELQLLALKVYWKYKLYCQQMQSVVASFETVAGLGHAAPYISFAFKAISKHFCCLK 70 (313)
Q Consensus 15 ~~l~~~l~ev~~ry~~y~~qmq~v~~sfe~~ag~g~a~~y~~lal~~~Sr~Fr~l~ 70 (313)
.+|..+.+..++=+++|+.+++..|..|+.+.-.-....+..+.-+.....+...+
T Consensus 36 ~~l~~~~~qa~~y~~~~~~elR~qv~~l~~~l~~v~~lv~~~~~~~~~~~~~~~~~ 91 (208)
T PF14644_consen 36 QKLQSYQEQADEYHNSCLQELRNQVERLEELLPKVPELVFESLLKRHWQKLCEAMK 91 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47888888899999999999999999999988666555555555554444444433
No 187
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=20.43 E-value=1.7e+02 Score=24.80 Aligned_cols=48 Identities=21% Similarity=0.194 Sum_probs=37.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhhchh
Q 040555 121 ALPDHAVAVLKTWLYENFLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRLWKP 176 (313)
Q Consensus 121 ~lp~~a~~iL~~wf~~h~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~kk~ 176 (313)
.||+..+.++...+.+ .+ .-.++|..+|++...|.+=...+|.++++-
T Consensus 140 ~L~~~~r~vi~l~~~~----g~----s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~ 187 (189)
T TIGR02984 140 KLPEDYREVILLRHLE----GL----SFAEVAERMDRSEGAVSMLWVRGLARLRQI 187 (189)
T ss_pred cCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4888888888775443 22 347899999999999999888888887653
No 188
>PF14978 MRP-63: Mitochondrial ribosome protein 63
Probab=20.29 E-value=3.5e+02 Score=22.01 Aligned_cols=35 Identities=17% Similarity=0.249 Sum_probs=27.5
Q ss_pred cCCCCCCHHHHHHHHHHhCCChHHHhhhhhhhHhhh
Q 040555 138 FLHPYPTDSDKQILAKQTGLSKNQVSNWFINARVRL 173 (313)
Q Consensus 138 ~~~PYPs~~eK~~LA~~tgLs~~QV~NWF~N~R~R~ 173 (313)
+.+||-|.++-...|+..+- ..+.-.|+..++.+.
T Consensus 37 Ls~PYLT~EQE~gh~~e~r~-~k~~~~~~~~~~~~k 71 (91)
T PF14978_consen 37 LSRPYLTAEQEYGHAKERRK-EKAFFEWIKEKKRSK 71 (91)
T ss_pred HcCCcccHHHHcchHHHHhH-HHHHHHHHHHHHHcc
Confidence 34999999999999988877 667777777776544
Done!